The Virus Project
2006-11-22
  Solid and/or Soup - a Virus in Water
Biological materials are very different from those studied by Classical Science.

Classical Science started with a very simplified set of assumptions; simply because nature is grand and complex, and it was necessary to ‘find a way in’ by starting to understand some simple issues first.

The assumptions that ‘matter is “inert”’ is perhaps the most crippling assumption still used in society. It was based on the assumption - and imposition – of the idea that the universe is “Invariant”. Inert.

The uniVerse is not Invariant; it is an ongoing process of development.
The uniVerse is neither Inert. Yet it can appear to us as such.

It must be kept in mind, that all we perceive is a mental construct.
“The Collapse of the Vector of State”, as Quantum Theory describes it, is the term that describes that the Observer defines and determines the Observation, by the type of involvement.

Thus the mode of involvement must be explicitly described, in order to be able to study and develop science.
Because, whatever we perceive, it is always the result of an interference pattern; of our state of being interacting with that of our context (of which we form part).

The dynamics of the Collapse of the Vector of State is determined by the model of an Interference pattern.
It is the result – in that model – of Constructive and Destructive interference (of waves) that builds the reality that we know. Our Reality is a Realisation.

What quantum theory describes, if it is to be uniVersally true, must apply to us also.
It must then also be valid for this exploratory study on the nature of the Virus.

We can summarise the findings as follows:
The universe, us included, is a wave field.
Every interaction and relationship is an interference pattern between wave fields in a wave field.

This then must apply to a Virus also.
This is why the study of the Virus here is held do apply to both the bio-organism (virus) and informatics code for computation (computer virus).

The construct of an Interference pattern is a clue to be pursued:
Constructive and Destructive interference leads to an Interference pattern of the Moiré type.

This means that we are dealing with a wave pattern within a wave pattern.
This is the basis for a description of Nesting and Embedding; fitting a part into a whole, i.e. relating an object into a context.

Bear in mind that in this approach there is no object separate from a context.
Every object is one with its context; but surrounded by a collapsed wave field of higher order (called a boundary; an interference pattern of wave fields).

It means that every object is a process (an interference pattern).
The relationship between the object and the relation of the object and the context is an interference pattern (process) also.

What then is object?
What is process?

To study this deeper, look as the relationship between a river and a bedding:
The river shapes the bedding, yet the bedding shapes the river.

Regard the same in the gulf streams of the oceans, and the jet streams of the atmosphere.
Likewise there are ionic currents – like smooth lightning snakes – in our ionosphere.

In an electric conductor we see the same: there are electrons of the current, and there are electrons of the atomic metal lattice. How can you tell them apart?

In water – a fluid crystal – we see the same:
water is coherent in droplets of 59 [nm] and incoherent (‘like boiling water’) in-between.

Herbert Fröhlich applied the understanding of atomic lattices of metal to study this.
He calculated the energy needed to liberate an electron from an atomic lattice.
(See “Herbert Fröhlich, FRS, a physicist ahead of his time, ISBN 0-906370-41-8)

In his studies he showed that we are not only dealing with electrons in a lattice; we are simultaneously dealing with the movement of lattices as a whole. Important is to realise that when particles move in a coherent manner (as fields as a whole) they can travel at speeds faster than light. This is a logical consequence of the phase propagation in and of a coherent field). In the description of materials this is called Superconductivity.

Last night I had a dream in which I was shown the relationship between cubic atomic crystals (such as found in a metal atomic lattice) and the free electrons between them. It was ‘explained’ to me, in my dream (an unconscious mental metabolic process) how the two were related. Upon waking I realised that soup referred to sup-er conductivity.

It is this notion that is relevant for this study of the Virus also.

The virus is a nano-tech antenna.
It functions in a context of water.

This means that the Virus presumably links with, maybe even interlocks with, the droplets of coherent water. I can imagine that the ‘legs’ off the virus connect to ‘droplets’ of coherent water.
The water droplets are like mini computers; they can store close to 1000 different frequencies (see the work of Cyril Smith). These frequencies can be matched as interference patterns (with constructive and destructive interference), thus function as logic gates (AND and OR, NAND and NOR gates).

Virus – in this conceptualization – operate these nano-computers.
They bring local coherence between water droplets: the virus serves a s circuit board in a primordial soup of informatics in water.

It is this kind of concept, in which a virus brings coherence in particular forms of coherence in water, that is to be further explored.

The particular forms of coherence in water, as the 59 [nm] droplets described by Cyril Smith.
The particular forms of coherence of the virus, is the antenna shape, and the near metallic structure of molecular coherence, in the form of the Virus.

What can be shown about the relationship between the Virus, and its presumable role in bringing coherence between coherent droplets of water.
The principles described by Fröhlich, about superconductivity in super-coherence will be valid.
Likewise it will be based on the same concepts as those of the ionic streams in the ionospheric ‘bedding”; and a river and a bedding.

It is the relationship between Potential and Kinetic energy (the coherent water, or molecular ‘boiling’ water) which is found also in the Cosmic Gas Cloud, and the Lightning Charge Discharges that compute the location of the stars.

It is all about the relationship between information and matter.
What we perceive in our living body, must be at the basis of the existence of the virus also…

Thence this exploration:
Is the Virus a primordial form of operator, operating on the information in water, in the coherent droplets described by Cyril Smith?

If so, it is likely that a virus is not a pathogen; because it simply computes and has no own mind or meaning.

What then changed in the development of the virus, that it could encapsulate itself, not in a protein sheath but is a double lipid membrane, to develop into a microbe: the bacterial form? (This presupposes an environment in which fatty soap bubbles could form. And engendered a micro environment in which the virus can compute and replicate by dividing itself.)

More questions
More answers
  09:18
2006-11-10
  Virus - From Physics to Phasics

Let us do a Reality Check

Many people wish to believe that the human body is a kind of machine. It is not.

Modern Medical Science is an obsolete belief system: the body is neither an object nor material. It does not follow the laws of inertial (thus causality, i.e. determinism as postulated by a set of over-simplifications). The body is an information system, in which the internal state is systematically recomputed in respect to the state change of the ambient context. The body adopts and adapts; in ways that no machine can yet do.

Some fundamental questions need to be raised.

We need to be able to relate the processing of information to abilities of adaptation.

We need to correlate changes in degrees of freedom, to changes in patterns of information organisation.

But more important than that that: we need to reconsider our total conceptualisation of medical science; we need to account for the state change that we see – and experience – in living bodies.

Extensive work has been done towards this. But ‘none’ of this work has yet been incorporated into the studies, or doctrines, of medical science.
Some of these insights will be presented. The following works relate to the electromagnetic dynamics in our living body.
They bring our understanding a lot closer toward the understanding which we now have of computable systems (computers).
They possibly help us to advance our conceptualisation of computer virus, towards the process dynamics that we find in living beings.

These books offer much more insight and depth than summarised above.

There are many other books that are very detailed and explicit in their description of the importance of electromagnetism in our body.

For example:

It does not make sense to regard our body as if these electrodynamic processes do not play a role.


We have however long since moved out of the era of electrics and electronics into the information era, of computation and informatics. Unknown to many we already likewise have passed through, and deeper into, the knowledge of radionics.
Many of these theories are unknown simply because science has to a large extent become a system of belief. People prefer to disregard and discard a model that ‘their’ model cannot understand, than apply themselves to the art of science: explore and study the unknown.

In dealing with our living body we cannot afford to be led by belief; we need to know.
We need to understand the basic dynamics of our body.

Science has come to conclude that matter is made up out of molecules which are composed of atoms which are created by interacting subatomic (immaterial) fields.
Information is the basis of our body.
We need to apply and use this understanding.

We do not have a body, organs or cells.
All what we experience is based on the interaction and interchange of the fields underlying atoms and molecules that form our body.

From a classical mechanical model of science, we are told that our body is formed out of Neutrons, surrounded by Protons, circled by Electrons, shepherded from one orbit to another by Photons.

Evidently this model is incomplete, or absurd: a photon at full speed cannot hit an orbiting electron, at full speed, with the accuracy and precision by which the electron will hop from one orbit to another. Statistical chances for such full speed particle hits are by far too small.

The particular view needs to be replaced by a model of waves, in which resonant frequencies are shifted from one harmonic to another, in interactive field systems.

It is this realisation that has been presented before: we need to regard virus as forms of stabilised waves.

However: the notion of solid state, stability, and invariant structure itself need to be discarded. The smaller the scale of detail, the higher its internal dynamics.

Matter, Molecules, Atoms, and Subatomic Field.

As the Alchemist described: the more we move into details,
the more the frequency needs to be raised.

Our body, at the smaller scales, is determined by ever more intense dynamics. It is not an object, process or transformation, but a system of dimensional transmutation.
Our body operates on changes of degrees of freedom. This is what I would expect to find also in any virus.

Virus is therefore unlikely to be a crystalline structure, as it is usually represented.
In fact the definitions of the virus show that crystallisation of the virus is difficult to achieve.

So, rather than regarding the virus as a structure, let us regard it as a process; and a specific kind of standing wave, or rather oscillation, probably even a wave modulation, in which an information field is maintained in a changing context.

This is what we would seek as the basis of life.

A combination of what we now know of the subatomic dynamics: the oscillations of pure waves of phase. But now, somehow, on a larger scale of manifestation, which could later lead to more elaborate and bulky forms of manifestation: from proteins to enzymes to RNA and DNA; and from virus to bacteria to eukaryote cells…


The hypothesis that I present herewith, is that our body is an electromagnetic process; not as an electronic circuit board but as a system of and for processing information.
Of which, I presume, the virus also is an example.
Which, when understood, can help us understand this.

Feel well

O#o

  21:29
  The Virus - Shaping a Wave Field?

Is the Virus – A standing Wave?

Perhaps we need to link up the concept of Sacred Geometry,
in/to the understanding of Virus.

Minerals do the same; the ordered atomic lattice ‘combs’ the ambient wave field to a coherent interference pattern of waves, around the mineral structure.
Gems, minerals with an atomic lattice with atomic doping, offer multiple different ordered lattices, thus can provide more complex filtering of the wave ambient field.
(They 'operate multiple wave bands', thus 'have more bandwidth'.)

(Doping is a technical term, for the insertion of – in this case atoms – into an existing substance.
A schema of “doping” can be visually presented as follows:

oooXoooXoooXoooXoooXoooXoooXoooXoooXoooXoooXoooXoooXoooXoooXoooXoooXoooXoooXoooX

Because of the existence of the ‘o’ atom lattice, the interspersed “X” lattice can be held in place (which otherwise could not exist in nature).
The result is that the ‘o’ wave field forms the ‘carrier wave’ for the “X” ‘Filter”.
(This principle is related to that of Holograms: a general and a specific frequency pattern interference.)
As a result, the “X”-grid can function, and order frequencies of the ambient wave field.)

Sacred Geometry describes the coherence of integral wave field.
The most basic form is that of a Vortex.
This is a basic form that defines dimensional transition.
In a Vortex a volume (e.g. bath), a plane (water surface), a line (vortex funnel) and a point (bath plug hole) are interconnected.

In sacred geometry, the interference of (phase) field is made explicit.
All forms are forms of relationships, forms of transformation, and forms of emergence.
This means that all forms relate to different forms of dimensional coherence.
This is precisely what is to be expected in life forms, which are forms of information, in formation.

In life forms, the essence is the manifestation of Freedom of Choice.
This equates to the ability to change the internal degrees of coherence,
This is expressed in terms of topological changes, between Dimensional States.
Life thus operates Dimensional (de)Compression; Sacred Geometry offers graphic representation.

Sacred geometry shows that a Vortex has an Envelope, a Stellate (star shape) and a Polygon, as equivalent formulations of the same concept.
This is to be expected:

a Vortex is the form that links the dimensional transmutations.
A Stellate is the topological sets of (singularity) points of contacts with the context.
The Polygon is the interface/membrane that can be drawn between the points of the stellate.
The Envelope is the interface where the interference pattern of the Vortex/involution interferes with the evolution of the context. It is field.

What we see is the interference field of interference fields of waves of waves.

Because we too are a field, we can only describe this in terms of field iteractions.
The only effective language for this is Integral Field theory, of which Superstring theory is an emergent example.
Quantum Theory can be used only if formulated in terms of a field, and accounting for human involvement
Relativity Theory can be used only of the limitation of the description is included in the description (The Tiller-Einstein solution of transcending the critical limits).
Classical Deterministic Theory can be used only as specific instance of a momentary perception. It is a frozen image of a film of development determined by observer involvement. This gives it only limited (subjective, personal, momentary, invariant) use. (In general this means it is useless for the understanding of life.)

Sacred Geometry can be regarded as a representation of a wave form. (Regard it as an ongoing film.)
The question is:

The answer of this will require precise calculations.

Crystallographers, have you done such calculations?
Astronomy antennae experts, can you offer suggestions?

Feel well

O#o

  10:50
  The Virus - Is it an Antenna?!
The formal definitions about a virus are too vague, to be of value.



Perhaps we can look for a more simple definition of a virus.
If a virus is not alive, nor dead, perhaps is is simply a form of information.
Perhaps it is just a simple form of a program. A form of information
We know it has a form; a form (pattern) of Vibration.
What is the form itself is its 'magic', the purpose and essence of what Virus is?

Let us backtrack:
Hypothesis is that the universe emerged from phase space.
Nothing is the basis of thing. Manifestation is a form of (in)formation.
Big Bang stands between them: and inversion from nothing to thing.

Cosmology is better understood by tracing the history of physics.
Matter was found to exist out of molecules composed of atoms; composed of subatomic fields.
Things were found to be based on no-things.
Another description of the same: Physics is Chemistry is Electromagnetic is Phasics.

Phasics is the clue; and the essence.
Phasics is the nature of Phase Space.
It addresses the essence of coherence, and existence.
Big Bang, Cosmic Gas, Stars and Planets traces the history of matter in inverse.

Big Bang: a phenomenon of Plasma.
Cosmic Gas, as the name spells: a Gas.
Stars, a manifestation as Fluid.
Planets: a Solid form of manifestation.

This was what the Alchemists studied.
Their interest was in Transmutation.
This we call now the transition between Degrees of Freedom.
We now describe this as a Logic of Dimensional Sets,

This is what we need to understand cosmology:
the transition from NoThing to Thing.
from plasma to gas to fluid to structure,
through different forms of manifestation.

This probably is the essence:
The form changes, but the essence does not.
The UniVerse is a unified field of Vibration.
Manifestation is simply an ongoing process of its expression.

Tracing back in time, we see that mater = molecules = atoms = plasma.
The form and nature of matter, is a form of subatomic coherence.
All that we know and perceive, is a pattern of vibration.
All is information in formation.

We see the same in the emergence of life forms.
Minerals lead to plants, to animals, to sapient sapient life forms.
In-between we see (Margulis, 1993) that the eukaryote cell emerged out of the fusion of four bacterial forms:
Earth, aqueous (Water), aerobic (Air) and photosynthetic (light, Fire)

The bacteria is however is already a com-plex.
It contains nuclear plasma, and a membrane.
It is already a form of a cell.
This is a quite complex geometrical form.



In other words: can we understand the bacteria as a development from the Virus?
Can we explain bacterial vital functions in term of viral characteristics?
Can we find a direct relationship between form and information?
Can we understand the (laws of) forms of transformation of information?



The hypothesis is: yes we can.
If we but look.

For this reason this project proposes that we regard the virus as an antenna, a program.
The reason for this is simple:
Experiment showed that electric charge discharge over a primordial soup formed Amino Acids.
What is Amino Acids are the trace of the Lightning, in matter. A Lightning conductor, a conduit, an antenna?


Ken Rand described the lightnings.
Phil Callahan described the antennae


It is known that Lightning is a computation.
It computes the geodesic (optimal pathway) of Charge Discharge.
Lightning links Time-Space. It jumps a fixed distance and waits a fixed time, always, again and again.
Lightning – from the Cosmic Cloud onwards – computes balance.

If Lightning and amino acids are linked; then charge-discharge is linked with a form of manifestation.
The emergence of more complex forms of molecules is then expression of more complex forms of manifestation.Once the lightning conductors have been created, they simply develop.
Let us regard lightning conductors in their more general form: antennae.

Antennae exist in many different forms.
Within them there is a flow of current: electric.
Around them, there is a shape of a field: magnetic.
Both are (inter)linked in the antenna.

In the antenna, there is a flow: a current: a rod…
Around the antenna there is a charge, a membrane…

A virus is a combination of Rods, and Membranes.
Let us simply regard the virus as a construct of antennae.
A construct of antennae: a mini circuit-board, in 3D.
What programs can it contain? What does it compute?

I welcome your suggestions.

Hackers, can you transcribe the shape of virus into ... computer programs?
The lengths of the rods and the shapes of the membranes specify the frequencies that the virus com-putes (integrates).
Integration is the essence of computation.
I presume that the virus hold a wave shape, stabilises electromagnetic vibration, which is significant, and the basis of life.


Feel well

O#o
  09:20
  Is this "a Virus"? (Wikipedia definition)
Virus
From Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Virus

In brief, the formulation is that a virus is genetic material in a capsid
(a capsid is a protein layer, not considered to be a membrane).
How does the capsid envelope get to be there?
What distinguishes it from a membrane?
So, the genetic material ... is considered to be dead?!



This article is about a biological infectious particle; for the computer term, see computer virus. For other uses, see virus (disambiguation).
?Viruses

Virus classification
Group:
I - VII
Groups
I: dsDNA virusesII: ssDNA virusesIII: dsRNA virusesIV: (+)ssRNA virusesV: (-)ssRNA virusesVI: ssRNA-RT virusesVII: dsDNA-RT viruses
A virus (Latin, poison) is a microscopic particle that can infect the cells of a biological organism. At the most basic level, viruses consist of genetic material contained within a protective protein coat called a capsid; the existence of both genetic material and protein distinguishes them from other virus-like particles such as prions and viroids. They infect a wide variety of organisms: both eukaryotes (animals, fungi and plants) and prokaryotes (bacteria). A virus that infects bacteria is known as a bacteriophage, often shortened to phage. The study of viruses is known as virology, and those who study viruses are known as virologists.
It has been argued extensively whether viruses are living organisms. Most virologists consider them non-living, as they do not meet all the criteria of the generally accepted definition of life. They are similar to obligate intracellular parasites as they lack the means for self-reproduction outside a host cell, but unlike parasites, viruses are generally not considered to be true living organisms. Among other factors, viruses do not possess a cell membrane or metabolise on their own. A definitive answer is still elusive because some organisms considered to be living exhibit characteristics of both living and non-living particles, as viruses do. For those who consider viruses living, viruses are an exception to the cell theory proposed by Theodore Schwann, as viruses are not made up of cells.
Contents[hide]
1 Discovery
2 Origins
3 Classification
4 Structure
4.1 Size
4.2 Genetic material
5 Replication
6 Lifeform debate
7 Viruses and disease
7.1 Epidemics
7.2 Detection, purification and diagnosis
7.3 Prevention and treatment
8 Applications
8.1 Life sciences
8.2 Materials science and nanotechnology
8.3 Weapons
9 Etymology
10 See also
11 External links
12 Footnotes
13 References
//

[edit] Discovery
Viral diseases such as rabies have affected humans for many centuries, but the cause of these diseases was discovered relatively recently. In 1717, Mrs Mary Montagu, the wife of an English ambassador to the Ottoman Empire, observed local women inoculating their children against Smallpox. In the late 18th century, Edward Jenner observed and studied Miss Sarah Nelmes, a milkmaid who had previously caught Cowpox was subsequently found to be immune to Smallpox, a similar virus.
In the late 19th century Charles Chamberland developed a porcelain filter. This filter was used to study the first documented virus, tobacco mosaic virus. Shortly afterwards, Dimitri Ivanovski published experiments showing that crushed leaf extracts of infected tobacco plants were still infectious even after filtering the bacteria from the solution. At about the same time, several others documented filterable disease-causing agents, with several independent experiments showing that viruses were different from bacteria, yet they could also cause disease in living organisms. The term virus was coined by the Dutch microbiologist Martinus Beijerinck.
In the early 20th century, Frederick Twort discovered that bacteria itself could be attacked by viruses. Felix d'Herelle, working independently, showed that a preparation of viruses caused areas of cellular death on thin cell cultures spread on agar. Counting the dead areas allowed him to estimate the original number of viruses in the suspension. Finally, in 1935 Wendell Stanley crystallised the tobacco mosaic virus and found it to be mostly protein. A short time later the virus was separated into protein and nucleic acid parts.

[edit] Origins
The origins of modern viruses are not entirely clear, and there may not be a single mechanism of origin that can account for all viruses. As viruses do not fossilise well, molecular techniques have been the most useful means of hypothesising how they arose. Research in microfossil identification and molecular biology may yet discern fossil evidence dating to the Archean or Proterozoic eons. Two main hypotheses currently exist[1]:
Small viruses with only a few genes may be runaway stretches of nucleic acid originating from the genome of a living organism. Their genetic material could have been derived from transferable genetic elements such as plasmids or transposons, which are prone to moving around, exiting, and entering genomes.
Viruses with larger genomes, such as Poxviruses, may have once been small cells which parasitised larger host cells. Over time, genes not required by their parasitic lifestyle would have been lost in a streamlining process known as retrograde-evolution or reverse-evolution. Both the bacteria Rickettsia and Chlamydia are living cells which, like viruses, can only reproduce inside host cells. They lend credence to this hypothesis, as they are likely to have lost genes enabling them to survive outside a host cell, in favour of their parasitic lifestyle.
Other infectious particles which are even simpler in structure than viruses include viroids, satellites and prions.

[edit] Classification
For more details on this topic, see Virus classification.
In taxonomy, the classification of viruses is rather difficult due to the lack of a fossil record and the dispute over whether they are living or non-living. They do not fit easily into any of the domains of biological classification and therefore classification begins at the family rank. However, the domain name of Acytota has been suggested. This would place viruses on a par with the other domains of Eubacteria, Archaea, and Eukarya. Not all families are currently classified into orders, nor all genera classified into families.
As an example of viral classification, the chicken pox virus belongs to family Herpesviridae, subfamily Alphaherpesvirinae and genus Varicellovirus. It remains unranked in terms of order. The general structure is as follows.
Order (-virales)
Family (-viridae)
Subfamily (-virinae)
Genus (-virus)
Species (-virus)
The International Committee on Taxonomy of Viruses (ICTV) developed the current classification system and put in place guidelines that put a greater weighting on certain virus properties in order to maintain family uniformity. In determining order, taxonomists should consider the type of nucleic acid present, whether the nucleic acid is single- or double-stranded, and the presence or absence of an envelope. After these three main properties, other characteristics can be considered: the type of host, the capsid shape, immunological properties and the type of disease it causes.
In addition to this classification system, the Nobel Prize-winning biologist David Baltimore devised the Baltimore classification system. This places a virus into one of seven Groups, which distinguish viruses based on their mode of replication and genome type. The ICTV classification system is used in conjunction with the Baltimore classification system in modern virus classification.

[edit] Structure
A complete virus particle, known as a virion, is little more than a gene transporter, consisting of nucleic acid surrounded by a protective coat of protein called a capsid. A capsid is composed of proteins encoded by the viral genome and its shape serves as the basis for morphological distinction. Virally coded protein units called protomers will self-assemble to form the capsid, requiring no input from the virus genome - however, a few viruses code for proteins which assist in the construction of their capsid. Proteins associated with nucleic acid are known as nucleoproteins, and the association of viral capsid proteins with viral nucleic acid is called a nucleocapsid.
In general, there are four main morphological virus types:
Helical viruses

Diagram of a helical capsid
Helical capsids are composed of a single type of protomer stacked around a central circumference to form an enclosed tube resembling a spiral staircase. This arrangement results in rod-shaped virions which can be short and rigid, or long and flexible. Long helical particles must be flexible in order to prevent forces snapping the structure. The genetic material is housed on the inside of the tube, protected from the outside. Overall, the length of a helical capsid is related to the length of the nucleic acid contained within it, while the diameter is dependent on the overall length and arrangement of protomers. The well-studied Tobacco mosaic virus is an example of a helical virus.
Icosahedral viruses

Electron micrograph of icosahedral virions
Icosahedral capsid symmetry results in a spherical appearance of viruses at low magnification but actually consists of capsomers arranged in a regular geometrical pattern, similar to a soccer ball, hence they are not truly "spherical". Capsomers are ring shaped structures constructed from five to six copies of protomers. These associate via non-covalent bonding to enclose the viral nucleic acid, though generally less intimately than helical capsids, and may involve one or more protomers.
Icosahedral architecture was employed by R. Buckminster-Fuller in his geodesic dome, and is the most efficient way of creating an enclosed robust structure from multiple copies of a single protein. The number of proteins required to form a spherical virus capsid is denoted by the T-number[2], where 60×t proteins are necessary. In the case of the hepatitis B virus the T-number is 4, therefore 240 proteins assemble to form the capsid.
Enveloped viruses

Diagram of enveloped HIV
In addition to a capsid some viruses are able to hijack a modified form of the cell membrane surrounding an infected host cell, thus gaining an outer lipid layer known as a viral envelope. This extra membrane is studded with proteins coded for by the viral genome and host genome, however the lipid membrane itself and any carbohydrates present are entirely host-coded.
The viral envelope can give a virion a few distinct advantages over other capsid-only virions, such as protection from enzymes and chemicals. The proteins studded upon it can include glycoproteins functioning as receptor molecules, allowing healthy cells to recognise these virions as "friendly", resulting in the possible uptake of the virion into the cell. Some viruses are so dependent upon their viral envelope that they fail to function if it is removed.
Complex viruses

Diagram of a bacteriophage
These viruses possess a capsid which is neither purely helical, nor purely icosahedral, and which may possess extra structures such as protein tails or a complex outer wall. Some bacteriophages have a complex structure consisting of an icosahedral head bound to a helical tail, the latter of which may have a hexagonal base plate with many protruding protein tail fibres.
The Poxviruses are large, complex viruses which have an unusual morphology. The viral genome is associated with proteins within a central disk structure known as a nucleoid. The nucleoid is surrounded by a membrane and two lateral bodies of unknown function. The virus has an outer envelope with a thick layer of protein studded over its surface. The whole particle is slightly pleiomorphic, ranging from ovoid to brick shape.

[edit] Size
To put viral size into perspective, a medium sized virion next to a flea is roughly equivalent to a human next to a mountain twice the size of Mount Everest. Some filoviruses have a total length of up to 1400 nm, however their capsid diameters are only about 80 nm. The majority of viruses which have been studied have a capsid diameter between 10 and 300 nanometres. While most viruses are unable to be seen with a light microscope, some are larger than the smallest bacteria and can be seen under high magification. Both scanning and transmission electron microscopes are commonly employed to visualise virus particles.
A notable exception to the normal viral size range is the recently discovered mimivirus, with a diameter of 400 nm. They also hold the record for the largest viral genome size, possessing about 1000 genes (some bacteria only possess 400) on a genome approximately 1.2 megabases in length. Their large genome also contains many genes which are conserved in both prokaryotic and eukaryotic genes[3]. The discovery of the virus has led many scientists to reconsider the controversial boundary between living organisms and viruses, which are currently considered as mere mobile genetic elements.

[edit] Genetic material
Both DNA and RNA are found in viral species, but generally a species will not contain both. One exception is the human cytomegalovirus, which contains both a DNA core and several mRNA segments. The nucleic acid can be either single- or double-stranded, depending on the species. Therefore viruses as a group contain all four possible types of nucleic acids: double-stranded DNA, single-stranded DNA, double-stranded RNA and single-stranded RNA. Animal virus species have been observed to possess all combinations, whereas plant viruses tend to have single-stranded RNA. Bacteriophages tend to have double-stranded DNA. Also, the nucleic acids can be either linear or a closed loop.

An electron micrograph of multiple polyomavirus virions
Genome size in terms of the weight of nucleotides varies quite substantially between species. The smallest genomes code for only four proteins and weigh about 106 daltons, while the largest weigh about 108 daltons and code for over one hundred proteins. Some virus species possess abnormal nucleotides, such as hydroxymethylcytosine instead of cytosine, as a normal part of their genome.
For viruses with RNA as their nucleic acid, the strands are said to be either positive-sense (also called plus-strand) or negative-sense (also called minus-strand) depending on whether it is complementary to viral mRNA. Positive-sense viral RNA is identical to viral mRNA and thus can be immediately translated by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA polymerase before translation.
All double-stranded RNA genomes and some single-stranded RNA genomes are said to be segmented, or divided into separate parts. Each segment may code for one protein, and they are usually found together in one capsid. Not all segments are required to be in the same virion for the overall virus to be infectious, as can be seen in the brome mosaic virus.

[edit] Replication
Viral populations do not grow through cell division, because they are acellular; instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves. They may have a lytic or a lysogenic cycle, with some viruses capable of carrying out both. A virus can still cause degenerative effects within a cell without causing its death; collectively these are termed cytopathic effects. Released virions can be passed between hosts through either direct contact, often via body fluids, or through a vector. In aqueous environments, viruses float free in the water.
In the lytic cycle, characteristic of virulent phages such as the T4 phage, host cells will be induced by the virus to begin manufacturing the proteins necessary for virus reproduction. As well as proteins, the virus must also direct the replication of new genomes, the technique used for this varies greatly between virus species but depends heavily on the genome type. The final viral product is assembled spontaneously, though it may be aided by molecular chaperones. After the genome has been replicated and the new capsid assembled, the virus causes the cell to be broken open (lysed) to release the virus particles. Some viruses do not lyse the cell but instead exit the cell via the cell membrane in a process known as exocytosis, taking a small portion of the membrane with them as a viral envelope. As soon as the cell is destroyed the viruses have to find a new host.
In contrast, the lysogenic cycle does not result in immediate lysing of the host cell, instead the viral genome integrates into the host DNA and replicates along with it. The virus remains dormant but after the host cell has replicated several times, or if environmental conditions permit it, the virus will become active and enter the lytic phase. The lysogenic cycle allows the host cell to continue to survive and reproduce, and the virus is passed on to all of the cell’s offspring.

A falsely coloured electron micrograph of multiple bacteriophages
Bacteriophages infect specific bacteria by binding to surface receptor molecules and then enter the cell. Within a short amount of time, sometimes just minutes, bacterial polymerase starts translating viral mRNA into protein. These proteins go on to become either new virions within the cell, helper proteins which help assembly of new virions, or proteins involved in cell lysis. Viral enzymes aid in the breakdown of the cell membrane, and in the case of the T4 phage, in just over twenty minutes after injection over three hundred phages will be released.
Animal DNA viruses, such as herpesviruses, enter the host via endocytosis, the process by which cells take in material from the external environment. Frequently after a chance collision with an appropriate surface receptor on a cell, the virus penetrates the cell, the viral genome is released from the capsid and host polymerases begin transcribing viral mRNA. New virions are assembled and released either by cell lysis or by budding off the cell membrane.
Animal RNA viruses can be placed into about four different groups depending on their mode of replication. The polarity of the RNA largely determines the replicative mechanism, as well as whether the genetic material is single-stranded or double-stranded. Some RNA viruses are actually DNA based but use an RNA-intermediate to replicate. RNA viruses are heavily dependent upon virally encoded RNA replicase to create copies of their genomes.
Reverse transcribing viruses are viruses that replicate using reverse transcription, which is the formation of DNA from an RNA template. Those viruses containing RNA genomes use a DNA intermediate to replicate, whereas those containing DNA genomes use an RNA intermediate during genome replication. Both types of reverse transcribing viruses use the reverse transcriptase enzyme to carry out the nucleic acid conversion.

[edit] Lifeform debate

Multiple rotavirus virions
Argument continues over whether viruses are truly alive. According to the United States Code, they are considered micro-organisms in the sense of biological weaponry and malicious use. Scientists however are divided. They have no trouble classifying a horse as living, but things become complicated as they look at simple viruses, viroids and prions. Viruses resemble life in that they possess nucleic acid and can respond to their environment in a limited fashion. They can also reproduce by creating multiple copies of themselves through simple self-assembly.
Viruses do not have a cell structure, regarded as the basic unit of life. They are also absent from the fossil record, making phylogenic relationships difficult to determine. Additionally, although they reproduce, they do not metabolise on their own and therefore require a host cell to replicate and synthesise new products. However, bacterial species such as Rickettsia and Chlamydia, while living organisms, are also unable to reproduce outside of a host cell.
An argument can be made that all accepted forms of life use cell division to reproduce, whereas all viruses spontaneously assemble within cells. The comparison is drawn between viral self-assembly and the autonomous growth of non-living crystals. Virus self-assembly within host cells also has implications for the study of the origin of life, as it lends credence to the hypothesis that life could have started as self-assembling organic molecules.
If viruses are considered alive, then the criteria specifying life will have been permanently changed, leading scientists to question what the basic prerequisite of life is. If they are considered living then the prospect of creating artificial life is enhanced, or at least the standards required to call something artificially alive are reduced. If viruses were said to be alive, the question could follow of whether other even smaller infectious particles, such as viroids and prions, would next be considered forms of life.

[edit] Viruses and disease
For more examples of diseases caused by viruses see List of infectious diseases
Examples of common human diseases caused by viruses include the common cold, the flu, chickenpox and cold sores. Serious diseases such as Ebola, AIDS, bird flu and SARS are all also caused by viruses. The relative ability of viruses to cause disease is described in terms of virulence. Other diseases are under investigation as to whether they too have a virus as the causative agent, such as the possible connection between Human Herpesvirus Six (HHV6) and neurological diseases such as multiple sclerosis and chronic fatigue syndrome. Recently it was also shown that cervical cancer is partially caused by papillomavirus, representing evidence in humans of a link existing between cancer and an infective agent[4]. There is current controversy over whether the borna virus, previously thought of as causing neurological disease in horses, could be responsible for psychiatric illness in humans[5].
Viruses have many different mechanisms by which they produce disease in an organism, which largely depends on the species. Mechanisms at the cellular level primarily include cell lysis, the breaking open and subsequent death of the cell. In multicellular organisms, if enough cells die the whole organism will start to suffer the effects. Although many viruses result in the disruption of healthy homeostasis, resulting in disease, they may also exist relatively harmlessly within an organism. An example would include the ability of the herpes simplex virus, which cause coldsores, to remain in a dormant state within the human body.

[edit] Epidemics
For more details on this topic, see List of epidemics.

The helical Ebola virus
A number of highly lethal viral pathogens are members of the Filoviridae. Filoviruses are filament-like viruses that cause viral hemorrhagic fever, and include the Ebola and Marburg viruses. The Marburg virus attracted widespread press attention in April 2005 for an outbreak in Angola. Beginning in October 2004 and continuing into 2005, the outbreak was the world's worst epidemic of any kind of viral hemorrhagic fever[6].
Native American populations were devastated by contagious diseases, particularly smallpox, brought to the Americas by European colonists. It is unclear how many Native Americans were killed by foreign diseases after the arrival of Columbus in the Americas, but the numbers have been estimated to be close to 70% of the indigenous population[7]. The damage done by this disease may have significantly aided European attempts to displace or conquer the native population. Viruses also cause some of the most dangerous diseases ever known to man, such as smallpox and AIDS.

The Marburg virus

[edit] Detection, purification and diagnosis
In the laboratory, several techniques for growing and detecting viruses exist. Purification of viral particles can be achieved using differential centrifugation, isopycnic centrifugation, precipitation with ammonium sulfate or ethylene glycol, and removal of cell components from a homogenised cell mixture using organic solvents or enzymes to leave the virus particles in solution.
Assays to detect and quantify viruses include:.

A viral plaque assay
Hemagglutination assays, which quantitatively measure how many virus particles are in a solution of red blood cells by the amount of agglutination the viruses cause between them. This occurs as many viruses are able to bind to the surface of one or more red blood cells.
Direct counts using an electron microscope. A dilute mixture of virus particles and beads of known size are sprayed onto a special sheet and examined under high magnification. The virions are counted and the number extrapolated to estimate the number of virions in the undiluted mixture.
Plaque assays involve growing a thin layer of host cells onto a culture dish and adding a dilute mixture of virions onto it. The virions will infect and kill the cells they land on, producing holes in the cell layer known as plaques. The number of plaques can be counted and the number of virions estimated from it.
Detection and subsequent isolation of new viruses from patients is a specialised laboratory subject. Normally it requires the use of large facilities, expensive equipment, and trained specialists such as technicians, molecular biologists, and virologists. Often, this effort is undertaken by state and national governments and shared internationally through organizations like the World Health Organization.

[edit] Prevention and treatment
Because viruses use the machinery of a host cell to reproduce and also reside within them, they are difficult to eliminate without killing the host cell. The most effective medical approaches to viral diseases so far are vaccinations to provide resistance to infection, and drugs which treat the symptoms of viral infections. Patients often ask for, and physicians often prescribe, antibiotics. These are useless against viruses, and their misuse against viral infections is one of the causes of antibiotic resistance in bacteria. However, in life-threatening situations the prudent course of action is to begin a course of antibiotic treatment while waiting for test results to determine whether the patient's symptoms are caused by a virus or a bacterial infection.

[edit] Applications

The polio virus

[edit] Life sciences
Viruses are important to the study of molecular and cellular biology as they provide simple systems that can be used to manipulate and investigate the functions of cells. The study and use of viruses have provided valuable information about many aspects of cell biology. For example, viruses have simplified the study of genetics and helped human understanding of the basic mechanisms of molecular genetics, such as DNA replication, transcription, RNA processing, translation, protein transport, and immunology.
Geneticists regularly use viruses as vectors to introduce genes into cells that they are studying. This is useful for making the cell produce a foreign substance, or to study the effect of introducing a new gene into the genome. In similar fashion, virotherapy uses viruses as vectors to treat various diseases, as they can specifically target cells and DNA. It shows promising use in the treatment of cancer and in gene therapy.

[edit] Materials science and nanotechnology
In April 2006 scientists at the Massachusetts Institute of Technology (MIT) created nanoscale metallic wires using a genetically-modified virus[8]. The MIT team was able to use the virus to create a working battery with an energy density up to three times more than current materials. The potential exists for this technology to be used in liquid crystals, solar cells, fuel cells, and other electronics in the future.

The reconstructed 1918 influenza virus

[edit] Weapons
For more details on this topic, see Biological warfare.
The ability of viruses to cause devastating epidemics in human societies has led to the concern that viruses could be weaponized for biological warfare. Further concern was raised by the successful recreation of the infamous 1918 influenza virus in a laboratory[9]. The smallpox virus devastated numerous societies throughout history before its eradication. It currently exists in several secure laboratories in the world, and fears that it may be used as a weapon are not totally unfounded. The modern global human population has almost no established resistance to smallpox; if it were to be released, a massive loss of life could be sustained before the virus was brought under control.

[edit] Etymology
The word is from the Latin virus referring to poison and other noxious things, first used in English in 1392. Virulent, from Latin virulentus "poisonous" dates to 1400. A meaning of "agent that causes infectious disease" is first recorded in 1728, before the discovery of viruses by the Russian-Ukrainian biologist Dmitry Ivanovsky in 1892. The adjective viral dates to 1948. Today, virus is used to describe the biological viruses discussed above and also as a metaphor for other parasitically-reproducing things, such as memes or computer viruses (since 1972). The neologism virion or viron is used to refer to a single infective viral particle.
The Latin word is from a Proto-Indo-European root *weis- "to melt away, to flow," used of foul or malodorous fluids. It is a cognate of Sanskrit viṣh "poison,", Avestan viš- "poison," Greek ios "poison," Old Church Slavonic višnja "cherry," Old Irish fi "poison," Welsh gwy "fluid"; Latin viscum (see viscous) "sticky substance" is also from the same root.
The English plural form of virus is viruses. No reputable dictionary gives any other form, including such "reconstructed" Latin plural forms as viri (which actually means men), and no plural form appears in the Latin corpus (See plural of virus). The word does not have a traditional Latin plural because its original sense, poison is a mass noun like the English word furniture, and, as pointed out above, English use of virus to denote the agent of a disease predates the discovery that these agents are microscopic parasites and thus in principle countable.

[edit] See also

Wikibooks has more about this subject:
Viruses, Prions, and Viroids (General Biology)

Wikimedia Commons has media related to:
Virus

Look up Virus inWiktionary, the free dictionary.
List of viruses
Nanobes
Nanobacteria
Provirus
Transduction

[edit] External links
Chart of viral pathogens which contribute to indoor air pollution
Viruses: The new cancer hunters - An IsraCast article on virotherapy
The Big Picture Book of Viruses - Pictures and general information on many viruses
Scientific American Magazine (October 2003 Issue) Tumor-Busting Viruses
Detailed genomic and bioinformatic information about Category A, B, and C priority pathogens at NIH-funded database.
Assorted information about Virus'

[edit] Footnotes
^ Prescott, L. (1993). Microbiology, Wm. C. Brown Publishers, ISBN 0-697-01372-3
^ http://rhino.bocklabs.wisc.edu/cgi-bin/virusworld/htdocs.pl?docname=triangulation.html
^ http://www.stanford.edu/group/virus/mimi/2005/Genome.htm
^ http://news.bbc.co.uk/2/hi/health/medical_notes/429762.stm
^ http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=10089006&dopt=Abstract
^ http://news.bbc.co.uk/2/hi/africa/4397891.stm
^ http://www.historylink.org/essays/output.cfm?file_id=5100
^ http://web.mit.edu/newsoffice/2006/virus-battery.html
^ http://www.cdc.gov/OD/OC/MEDIA/pressrel/r051005.htm

[edit] References
Icosahedral virus structure
All the Virology on the WWW
University of Leicester online notes - Virus Structure
Chronic Active Human Herpesvirus-6 (HHV-6) Infection: A New Disease Paradigm
Gelderblom, Hans R. (1996). 41. Structure and Classification of Viruses in Medical Microbiology 4th ed. Samuel Baron ed. The University of Texas Medical Branch at Galveston. ISBN 0-9631172-1-1
Radetsky, Peter (1994). The Invisible Invaders: Viruses and the Scientists Who Pursue Them. Backbay Books, ISBNs 0316732168 (hc), 0316732176 (pb).
Theiler, Max and Downs, W. G. (1973). The Arthropod-Borne Viruses of Vertebrates: An Account of the Rockefeller Foundation Virus Program 1951-1970. Yale University Press.
This article contains material from the Science Primer published by the NCBI, which, as a US government publication, is in the public domain
Retrieved from "http://en.wikipedia.org/wiki/Virus"
Categories: Viruses Virology English words of foreign origin Latin words
  01:07
hypothesis: we emerged out of the virus. A virus is not a pathogen, but nanoprocessor; and alive. By combining insights of virus and computer virus, can we come to understand life : the integration of information in matter; with freedom of choice. !

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