FAQ #4: VIRUSES

.1. ARE VIRUSES REAL & DO THEY CAUSE DISEASE?

Yes, viruses are real & some of them do cause disease. (The following is a first step toward proof. The second step is at the end of this post.)

Step 1. How Scientists Identify a Virus

https://www.webmd.com/a-to-z-guides/how-scientists-identify-virus

Many people wonder just how scientists know that the cause of SARS is a virus and, more importantly, this particular virus. Public health scientists verified that a common virus -- a coronavirus -- that has become more severe as the likely cause of severe acute respiratory syndrome (SARS). Many people wonder just how scientists know that the cause is a virus and, more importantly, this particular virus.

In 1890, Robert Koch described the basis rules that scientists use to determine if an infectious organism causes a specific disease. These four rules are called "Koch's postulates."

The organism must be found in people with the disease and be absent in people without the disease.

The organism must be able to be grown from tissues or other specimens from the affected individual in the laboratory.

The organism must cause the disease when given to an unaffected healthy person.

The organism must again be grown from this second individual.

In the case of SARS, we know that the coronavirus had been found and grown from several individuals who have been sick with the symptoms of SARS -- thus fulfilling the first two of Koch's postulates. Because it would be unethical to expose people with the virus, public health scientists use a science called epidemiology to prove that only people exposed to the virus have gotten the infection. This technique relies on interviewing and studying groups of people who have gotten ill and comparing them with people who have not come down with the disease. Investigators then assume the disease would occur if a person were exposed to the disease. They then look to see if newly unintentionally exposed people come down with the disease and that organism is grown from them. This fulfills in principle Koch's third and fourth rules.

In the case of SARS, scientists have clearly shown that the virus is associated with people with the disease and the virus has been isolated from these patients. The epidemiology also shows that the disease occurs in people who are exposed to the disease more often than people who have not been clearly exposed to the disease. Finally, the virus has been grown from the people who were subsequently exposed. In addition, scientists can use animals to demonstrate these last two rules by exposing the animal to the coronavirus and see if it causes a disease like SARS.

See further reading below for more detailed explanation and better proof.

.2. WHAT ARE VIRUSES?

A virus is DNA or RNA in a protein or lipid coating, in which the DNA or RNA is coded for injection on contact into animal or plant cells and for using the cell’s DNA to replicate the virus until the cell is so full of viruses that it bursts, killing the cell and dispersing the viruses.

.3. WHAT ARE THE COVID RNA SEQUENCES THAT CODE FOR INJECTION INTO CELLS?

(to do)

.4. WHAT ARE THE COVID RNA SEQUENCES THAT CODE FOR COMMANDEERING A CELL’S DNA?

(to do)

.5. HOW DOES THE VIRUS COMMANDEER THE CELL’S DNA?

(to do)

Step 2. How do we know that Viruses exist?

https://insidecorona.net/how-do-we-know-that-viruses-exist/

What exactly was responsible for diseases like rabies? Was the pathogen comparable to bacteria, or just so very alien in nature that it would not compare to anything known until then? Was it even physical in nature?

One of the persons who came one step closer to the answer for these questions was the French microbiologist Luis Pasteur, who lived in the 19th century. Previous successes with anthrax and fowl cholera established him as an icon in medicine and microbiology. But his meticulous search for the pathogen responsible for rabies was fated to be unsuccessful from day one, since none of the responsible pathogens could ever have been seen with the microscopy techniques of the time.

Given the disease’s severe nature and lethality, Pasteur tried to develop a vaccine against rabies, despite the fact that there was no hint on a pathogen’s existence except the symptoms it caused. Drawing on his experience with bacterial pathogens he eventually succeeded to develop an effective vaccine. He circumvented the need to isolate the pathogen by using infected nerve tissue to pass the disease to different mammal species like rabbits and dogs, reducing its virulence with every cycle. Just a few years later after successfully testing it on dogs - in 1885 - the vaccine saved the life of the 9-year-old French boy Joseph Meister, making him the first person ever to be immune to rabies.

So, even when the true nature of the rabies pathogen remained a mystery, Pasteur was still able to prevent it from infecting people (and dogs), just by carefully observing the matter at hand, and learning from the way bacteria work. The fact that this technique worked implied that this pathogen was interacting with our bodies in a similar way to bacteria, proving that it must be physical in nature and hence we must be able to find it.

The development of the Chamberland filter, by Charles Chamberland, one of Pasteur’s assistants at the time, narrowed the physical properties of the pathogen down further. The filter basically consists of a porcelain tube with an opening on one side through which a liquid can be filtered, provided sufficient pressure.

This filter was shown to separate observable microorganisms from the liquid, including pathogenic bacteria. In 1892, Russian biologist Dimitry Iwanowski, who was investigating the mosaic disease of certain plants, filtered juice from infected leaves with the Chamberland filter and documented that the extracted juice was still infectious to healthy tobacco plants. He also observed that, unlike disease-inducing bacteria which would lose their ability to survive after a short time without nutrients, the filtrate remained infectious for many months after the filtration process. This not only added further evidence to the true nature of viruses but incidentally foreshadowed one of viruses' most annoying traits: The ability to survive without any kind of metabolism, akin to plants, animals or bacteria.

This experiment was repeated with many other diseases in the following years, including rabies. Dutch microbiologist Martinus Beijerinck first introduced the word “virus” for the filtered infectious liquid in 1898 (From Latin virus: "poison, slime, venom"). And although scientists were still uncertain if viruses were liquid or composed of particles, these experiments demonstrated that the responsible pathogens must be soluble in water and small enough to pass the Chamberland filter. This is a prime example of how scientists can demonstrate the existence of something from its effects on its environment under controlled conditions, which may even permit educated guesses about its nature.

But as they say: “Seeing is Believing”, (not "Educated Guessing is Believing") so let’s proceed with our hunt for specifically visible proof with:

Indication 2: Evidence by Visualization

In the years after the discovery of the infectious liquids called “viruses” microscopy techniques improved more and more, to the point where clumps of multiple virus particles could be shown. Some scientists supposedly saw these clumped viruses without knowing it to be viruses; but the resolution and magnification abilities of light microscopes were nowhere near high enough to determine any kind of structure. There is a physical limit to the magnification a microscope can achieve. To discuss this limit, we must digress a bit and take a closer look on how waves work, and how light and matter interact:

Light can be seen as a wave. Reflection, diffraction and refraction alongside things like absorption and emission are the main interaction mechanisms between this wave and matter and they allow us to see. However, all these mechanisms depend on some level on the compared size between the wavelength and the object. Smaller objects would just be “ignored” by the wave. Since waves of any kind share some of their basic principles, a comparison with water waves can come in handy to visualize this property: Imagine boulders disrupting the waves on a beach. One could deduce the boulder's existence and make assumptions on their size by the way the waves move past these boulders and arrive on the beach. Now imagine a 20 m high super wave, which would just sweep over them and not show any sign of their existence. Similarly, electromagnetic waves ignore obstacles that are much smaller than the wavelength.​*​ This is the reason why viruses are being “ignored” by the light waves used in light microscopy. To be precise: The spectrum of visible light (which is most commonly used in light microscopy) covers wavelengths from roughly 700 nm down to ca. 400 nm. Considering the just discussed dependence of light-matter interaction on size and the way a microscope guides its light, adding the application of some math, we find the highest theoretical resolution in light microscopy to be calculated around 250 nm. Even today, however, a great expense of resources and effort must be spent to come close to this level of resolution. Most viruses are much smaller. The SARS-CoV-2 virus measures in at roughly 120 nm diameter, less than half the theoretical limit!

Now, since light microscopy cannot let us see viruses, what other way might there be to make them visible to us, on our hunt for the visible proof of viruses existence?

Enter the Electron Microscope:

This revolutionary device was first built by German scientists Max Knoll and Ernst Ruska in 1931. This was shortly after French physicists Lois de Broglie’s hypothesis that particles can also behave like waves went ‘viral’ in 1923. The electron microscope takes this concept and circumvents the electromagnetic wavelength problem by waving electromagnetic waves goodbye and using the wave behaviour of accelerated electrons instead. Here, the lenses which focus the light were replaced with magnetic lenses in order to focus electrons (which are charged negatively). These coil arrays produce magnetic fields that bend the pathway of the electrons. After having passed the sample, and another magnetic lens, the electrons are detected by a fluorescent screen, which translates the signals of the incoming electrons into signals we can see. Since one could theoretically accelerate the electrons to velocities very close to the speed of light - thereby shortening their wavelength more and more - the theoretical resolution limit for electron microscopes is basically unlimited.

However, relativistic effects, exponentially growing energy costs for acceleration close to the speed of light, and technical aspects of magnetic lenses limit the practical resolution limit of modern electron microscopes to some still mind blowing 0.1 - 0.2 nm.

The electron microscope opened doors to deeper and smaller levels of the microcosmos for the scientific community, and as fate would have it, the brother of Ernst Ruska, Helmut Ruska, happened to be a physician and biologist. Very soon, he realized his brother’s inventions potential for microbiology, and together with their colleague Bodo von Borries they published the first microscopic picture of a virus in 1938.

And the new Coronavirus?

Fast forward to 2020: electron microscopy developers were not sleeping. In the 80 years that have passed since the brothers Ruska, many new methods have been developed and existing techniques were refined. And so, after the emergence of a new Coronavirus in the beginning of 2020, it was just a matter of time until EM pictures of SARS-CoV-2 were published. With this we can both see and believe SARS-CoV-2 exists!

See also: A pneumonia outbreak associated with a new coronavirus of probable bat origin https://www.nature.com/articles/s41586-020-2012-7