Open this accordion to see videos of the 2020-1028 virus talk

 

 

 

This is part 1 of our Zoom talk "Are viruses good or bad?" Some viruses will kill you if you don’t kill them first, but most viruses cannot harm us. Beneficial viruses may foster evolution, enhance biodiversity, and fight climate change and ocean acidification. Our NetLogo game simulates marine bacteriophages.

Viruses are not living cells, but particles that contain genetic material in a protein coat that infect cells to make more virus particles. Viruses are everywhere but most viruses are not harmful to us because they are highly specialized to infect bacteria or other organisms. Even bacteria have an immune system that can recognize some viruses and destroy them.

Lytic viruses destroy cells after taking over the genetic machinery and replicating themselves. Lysogenic retroviruses influence evolution by adding genetic material to the DNA of germ cells. For example, retrovirus DNA resulted in mammalian placentas. Our immune systems are very powerful and vaccines boost them.

 

This video is an example of the game we play with our NetLogo model of virus bacteria interactions

This is part 2 of our Zoom talk "Are viruses good or bad?" Some viruses will kill you if you don’t kill them first, but most viruses cannot harm us. Beneficial viruses may foster evolution, enhance biodiversity, and fight climate change and ocean acidification. Our NetLogo game simulates marine bacteriophages.

We can learn a lot about how infections spread by playing our NetLogo game. The game is based on marine viruses and cyanobacteria and can also help us understand how viruses affect evolution and enhance biodiversity. Our virus bacteria NetLogo game is a highly oversimplified model that exemplifies what statistician George Box said, that all models are wrong, but some are useful. Our model shows how populations surge and crash, the advantages of social distancing, and the potential effects of the evolution of viruses and immune systems.

 

 

This is part 3 of our Zoom talk "Are viruses good or bad?" Some viruses will kill you if you don’t kill them first, but most viruses cannot harm us. Beneficial viruses may foster evolution, enhance biodiversity, and fight climate change and ocean acidification. Our NetLogo game simulates marine bacteriophages.

Viruses are beneficial to life on our planet because they promote evolution by transferring genes, help evolution by eliminating losers, enhance biodiversity by restraining winners and by adding nutrients. They help fight climate change by controlling carbon dioxide. Carbon dioxide in the atmosphere warms the Earth by absorbing infrared light. Cyanobacteria and algae make food from carbon dioxide and water and sunlight just like land plants. Marine viruses help bury carbon in the seafloor. They help fight ocean acidification by controlling the amount of carbon dioxide dissolved in oceans which is acidic and dissolves carbonate seashells.

 

This is an earlier video of our NetLogo virus bacteria game.

 

 

Are viruses good or bad? What do they do?

Are they good or bad? Viruses harm individuals, but viruses may benefit the species overall by eliminating the least fit individuals. Viruses affect carbon cycles and climate. Viruses affected the origin and evolution of life. The only life on Earth for two billion years were small single cells of bacteria. Later some viruses evolved that attack the larger complex cells of fungus, algae, plants, or animals. Most viruses still only attack bacteria. Viruses even affected our own evolution. Although we regularly hear the negative effects of viruses, they are generally beneficial to the planet and to all species on Earth.

What do viruses do? Viruses don’t do anything until they encounter a living cell. Viruses invade living cells to make more viruses. Their genetic material takes over the cell’s replication machinery in order to make many more copies of the virus. Most viruses are lytic which means that the host cell is destroyed so that the virus copies can escape and spread. In some cases they escape without destroying the cell. Some viruses are lysogenic which means they simply embed genetic code in the cell’s DNA without destroying the cell. If the cell they embed their code in is a sperm or egg, then the genes are passed onto all of their descendants.

Could Giant Viruses Be the Origin of Life on Earth?

The ancestors of modern viruses may have laid the groundwork for cellular life as we know it.

https://www.nationalgeographic.com/news/2014/7/140716-giant-viruses-science-life-evolution-origins/

Scientists thought that viruses emerged after the appearance of cells because they rely on cells for replication. Modern viruses can't exist without cells. The ancestors of modern viruses may have preceded cellular life, may have provided the raw material for the development of cellular life, and almost certainly advanced the diversification of organisms throughout the planet. Giant viruses exemplify how simple virus-like elements could evolve into something much more complex. Virus-like elements may have had key roles in the emergence of life including the evolution of DNA, the formation of the first cells, and the diversification into the three domains, archaea, bacteria, and eukaryotes.

Viruses: their extraordinary role in shaping human evolution

https://www.sciencefocus.com/the-human-body/virus-human-evolution/

Viruses have had a huge influence on our human species. Around 50% to 80% of the human genome is suspected of being made up of millions of DNA sequences known as transposons that came from ancient extinct viruses. Most of the repetitive virus-derived DNA in the human genome is ‘junk’ or serves no function, but a close look at individual viral elements suggests that some of the viruses embedded in our genome have been repurposed to perform very important functions.

Syncytin  is a human gene whose only function is to make a molecule that fuses placental cells together, creating a special layer of tissue known as a syncitium. Another syncytin gene is also involved in forming the placenta as well as preventing the mother’s immune system from attacking the fetus in her womb. Both of these syncytins appear to have come from a retrovirus gene. Different syncytin genes seem to have been repurposed by other placental mammals.

Viruses are full of DNA sequences that attract molecules that switch genes on. In a functional retrovirus, these molecules activate the viral genes so it can become infectious again. When a virus-like sequence gets spliced into another region in the genome, it can act as a genetic switch for other functions.

There is an endogenous retrovirus in the human genome that came from a virus that infected our ancestors about 50 million years ago that detects a molecule called interferon that warns the body that it is suffering a viral infection. The infected cells are forced to self-destruct to stop the infection from spreading. These ancient viruses help defend our cells from other viruses.

The Viruses That Made Us Human

https://www.pbs.org/wgbh/nova/article/endogenous-retroviruses/

When the dinosaurs went extinct 65 million years ago, mammals had already been evolving for 100 million years. Like modern mammals, they had body hair and mammary glands, but the placenta did not evolve until a chance encounter with a retrovirus that infected one of our ancestor’s sperm or egg cells and passed its genes on to every cell in every subsequent generation. Copies of these genes may have been inserted in multiple places causing variations in gene expression throughout the development of an embryo.

Viral DNA resulted in the formation of a placenta that enables a fetus to develop inside a mother’s uterus. The placenta permits oxygen and nutrients to flow from the mother’s blood to the blood of the fetus and for waste to go the other way by keeping the blood supplies of the two organisms separate but in close contact.

Quote from the article: “Syncytin is produced only by certain cells in the placenta, and it directs the formation of the cellular boundary between the placenta and maternal tissue. Approximately one week after fertilization, the egg, now a hollow ball of cells called a blastocyst, implants itself into the uterus, stimulating the formation of the placenta, which provides the fetus with oxygen and nutrients while removing carbon dioxide and other wastes. It also serves as a barrier to prevent infection and keep maternal and fetal blood separate. Mixing the two could cause a fatal autoimmune response. The cells in the outer layer of the blastocyst form the outer layer of the placenta, and those in direct contact with the uterus are the only ones that made syncytin.”

Renee Reijo Pera discovered that the insertion of retroviral DNA in the right location in the genome can help control the expression of nearby genes. Slight shifts in the timing of certain developmental events of pluripotent embryonic stem cells can actually change development dramatically, especially during the first week after fertilization when rapid changes that occur. What used to be called junk DNA actually modulates development.

Human endogenous retrovirus HERV-K DNA is active around the time when the embryo is just eight cells. HERV-K was inserted as recently as 200,000 years ago. It’s so new that several of its copies in the human genome can still produce viral protein. To prevent this, adults keep a tight control on HERV-K by switching it off. HERV-K activates key genes that help transform a single cell into a fully-formed infant and help protect the tiny ball of cells from being infected by other viruses. HERV-H produces RNA molecules that switch other genes on and off. The 13 HERV-H switches identified by Reijo Pera and Wysocka team help keep the early embryonic cells pluripotent, ready for any job as an adult cell.

Ancient Viruses, Once Foes, May Now Serve as Friends

https://www.nytimes.com/2015/04/23/science/ancient-viruses-once-foes-may-now-serve-as-friends.html

paraphrased from the article

Our genomes are riddled with the detritus of ancient viruses. They infected our hominid ancestors tens of millions of years ago, inserting their genes into the DNA of their hosts. Today, we carry about 100,000 genetic remnants of this invasion. So-called endogenous retroviruses make up 8 percent of the human genome.

Mostly, these genetic fragments are generally nothing more than molecular fossils. Over thousands of generations, they have mutated so much that they cannot replicate in our cells. Our cells keep the viral DNA muzzled to minimize the harm it might cause. Endogenous retroviruses do wake up, and at the strangest time.

Endogenous retroviruses spring to life in the earliest stages of the development of human embryos. The viruses may even assist in human development by helping guide embryonic development and by defending young cells from infections by other viruses. Viruses may be playing a vaccine role inside the cell.

When an ordinary retrovirus infects a cell, it inserts its genes into the cell’s DNA. The cell then makes new retroviruses by making a copy of the virus’s genes as RNA molecules. The cell uses some of those RNA molecules to make proteins for the virus. Those proteins form a shell around the other RNA molecules, which become the new virus’s genes.

Embryonic cells produce RNA molecules from certain endogenous retroviruses lurking in the genome. Do retroviruses come out of hiding to take advantage of their young hosts when their defenses are weak? Or are these just biochemical accidents — embryonic cells mistakenly turning viral genes into RNA, then destroying their molecular mistakes?

When Joanna Wysocka investigated how a single fertilized egg turns into the hundreds of different types of cells in the human body, she discovered that embryonic cells turn to their viral genes at a specific time in the development of an embryo.

In the early stages of development, an embryo is largely made up of cells that can potentially become any sort of tissue. Over the course of many divisions, the cells continue to hold on to this potential. A protein called Oct4 latches on to DNA in order to turn genes on and off. One of Oct4’s favorite targets was a kind of endogenous retrovirus called HERV-K.

Oct4 triggers cells to make RNA from the viral genes. The embryonic cells then used some of the viral RNA to make proteins. The proteins were assembled into particles that bore a striking resemblance to retroviruses; some even budded off the surface of the cells, as viruses do.

Embryonic cells make HERV-K viruses for only a few days. They stop around the time an embryo implants on the wall of the uterus. During this window, the viruses alter embryonic cells in some potentially important ways.

A cell can sense new viral genes floating around its interior. It can respond to this threat by creating immune defenses against more invasions. Dr. Wysocka found that when HERV-K reawakens, the embryonic cell builds proteins on its surface that help ward off other viruses that may be trying to get inside.

The retroviral genes may even be guiding the development of embryos. Proteins made from HERV-K’s genetic instructions ferry some of the cell’s own RNA to its protein-building factories. The viruses may alter the balance of available proteins at a pivotal time during development — right when a clump of cells is going to turn into a complex body.

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Lytic vs. Lysogenic Cycles in Viruses

Viruses can either follow a lytic cycle of quick replication to an on-site lysis of the host cell, or can follow a lysogenic cycle in which they act as retroviruses, embedding the viral code into the genetic material of the host cell’s genome.

The lytic cycle is mainly seen in bacteriophage viruses, or viruses that only infect bacteria cells. The lytic cycle is characterized as the host cell being opened or lysed after immediate replication of the virion. Post lysis, the newly formed virions encounter a new host cell. The lytic cycle is seen more in viruses that do not have an envelope surrounding their capsid. One example of a lytic virus is COVID-19.

The lysogenic cycle is characterized by a delay in lysing of the host cell or the escape of newly formed viruses. The viral genome will integrate itself into the genome of the host cell and will be able to be replicated every time the cell undergoes mitosis or replicates itself. The virus inside of the cell can experience a period of latency where the virus is not replicated or expressed in the genetic material of the cell. When host cell conditions begin to deteriorate, the virus can then become more active, most likely because there is signaling that the virus must find a new host in order to continue to reproduce and infect. Viruses that preform the lysogenic cycle are also known as retroviruses and have the potential for altering generations.

Retroviruses are a key aspect of the evolution of mammals, especially humans. If the retrovirus infected a germ cell originally (sperm or egg cell), and implants its DNA into that genome, the viral genetic material will be passed onto all replications of that cell. These cells can combine during sexual reproduction to create offspring, these offspring will have the viral genetic bacteria in their genome without actually being infected by the virus themselves.

Wikipedia says “Lysogeny, or the lysogenic cycle, is one of two cycles of viral reproduction (the lytic cycle being the other). Lysogeny is characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome or formation of a circular replicon in the bacterial cytoplasm. In this condition the bacterium continues to live and reproduce normally. The genetic material of the bacteriophage, called a prophage, can be transmitted to daughter cells at each subsequent cell division, and at later events (such as UV radiation or the presence of certain chemicals) can release it, causing proliferation of new phages via the lytic cycle. Lysogenic cycles can also occur in eukaryotes, although the method of DNA incorporation is not fully understood.

“The difference between lysogenic and lytic cycles is that, in lysogenic cycles, the spread of the viral DNA occurs through the usual prokaryotic reproduction, whereas a lytic cycle is more immediate in that it results in many copies of the virus being created very quickly and the cell is destroyed. One key difference between the lytic cycle and the lysogenic cycle is that the lysogenic cycle does not lyse the host cell straight away. Phages that replicate only via the lytic cycle are known as virulent phages while phages that replicate using both lytic and lysogenic cycles are known as temperate phages.

“In the lysogenic cycle, the phage DNA first integrates into the bacterial chromosome to produce the prophage. When the bacterium reproduces, the prophage is also copied and is present in each of the daughter cells. The daughter cells can continue to replicate with the prophage present or the prophage can exit the bacterial chromosome to initiate the lytic cycle. In lysogenic cycle the host DNA is not hydrolysed but in lytic cycle the host DNA is hydrolysed in the lytic phase.”

 

Are they alive? How do they die? Do they evolve?

Are viruses alive? Viruses are not exactly alive because they cannot reproduce outside of a host cell and they don’t perform any metabolic functions on their own like producing or consuming materials or energy. Simple viruses are particles made out of genetic material inside a protein coating. The protein coat may be an icosahedral or helical rod arrangement of many copies of the same protein. The genetic material may be single strand or double strand DNA or RNA.

Viruses can be many different shapes and sizes that normally correlate to the host cell that they infect. Although there are many different structures or morphs of viruses, all viruses have the same common structures. A capsid membrane that is made out of proteins called capsomeres, which act as building blocks to build the capsid structure and genetic material which can be: single stranded RNA, double stranded RNA, single stranded DNA, or double stranded DNA.

There are three main shapes that viruses take:

Helical: single type of capsomere that are stacked around a central axis to form a helical structure which may have a hollow inside, or central cavity

 

Icosahedral: the capsid has 20 triangular faces through the arrangement of 2-5 capsomeres per face.

Prolate: an icosahedron elongated along one axis and is a common arrangement of the heads of bacteriophages.

There is a fourth shape that is called Complex: The capsid of these viruses is not perfectly helical nor icosahedral. They may also have extra protein structures such as protein tails or more walls surrounding the virus.

How do viruses die? Technically, viruses don’t die. Not because they are real-life zombies, but because they aren’t alive in the first place. The only way to destroy a virus is to make it so they cannot continue to replicate using a host cell. Viruses cannot die, because they are not alive. They can however, be inactivated or destroyed to a point where they cannot reproduce through the process of denaturing the viral proteins. Denaturing proteins happens through exposure to unideal conditions such as high or low temperatures, or a change in pH. In the ocean, if a virus doesn’t die of natural causes or infect a cell, it most likely gets eaten by a filter feeder.

One way to destroy a virus is through a process called denaturation. Denaturation is when proteins are exposed to non-ideal conditions, leading to them not being able to function. Examples of scenarios when proteins are denatured are in very hot conditions, very cold conditions, or when the proteins are exposed to new and harsh chemicals that alter the natural pH of the virus.

Viruses are made predominantly of proteins, leaving them high susceptible to being denatured. When viruses are exposed to temperatures above or below their specific ideal conditions, or to harsh chemicals, the viral proteins will denature, rendering the virus “dead”. Viruses that have the extra protein envelope are more likely to be denatured then viruses without one, as there are more proteins being exposed to an environment that could possibly not be ideal.

To quote Wikipedia, "Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity". It is the folded structure rather than the chemical composition that enables a protein to perform its functions. For more information, see https://en.wikipedia.org/wiki/Protein_folding, https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology, https://en.wikipedia.org/wiki/Peptide, https://en.wikipedia.org/wiki/Biopolymer, and https://en.wikipedia.org/wiki/Enzyme.

Do viruses evolve? Viruses have the ability to rapidly mutate which makes them able to evolve rapidly to be better suited to their host cell and environmental conditions. complex viruses co-evolved with their host cells. Species evolved immune systems to fight viruses, bacteria, and toxins. Some viruses alter genes of heir host cells which can be inherited by later generations.

The Khan Academy says "Viruses undergo evolution and natural selection, just like cell-based life, and most of them evolve rapidly. When two viruses infect a cell at the same time, they may swap genetic material to make new, "mixed" viruses with unique properties."

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How many viruses are there? Who do they infect?

Viruses are among the most numerous particles on the planet. There are more viruses on Earth than there are stars in the universe, specifically, 100 million times more. Viruses are so abundant due to their simple yet very effective way of reproducing more viruses, as well as their evolved ability to infect every living thing on Earth.

Although it is estimated that there are 10 nonillion viruses (10 to the 31st power), scientists have only discovered 200 strains of viruses that are able to infect humans and cause illness. The other millions of viruses on Earth infect other animals, plants, and mainly bacteria.

Viruses are very successful at reproduction and evolution. This success has led them to be one of the most abundant (almost) living organisms on Earth. Because viruses are so small and in all of the nooks and crannies of the Earth, some scientists believe that we have only just begun to count the number of viruses on Earth. In reality, there can be a much, much larger amount than we currently think.

Viruses have been found to infect every branch of life on Earth. There are specific viral strains that have evolved to infect eukaryotes (organisms with many cells, such as humans), prokaryotes (single celled organisms), and archaea. There have even been strains of viruses found that infect other viruses!

Viruses have evolved to be very specific to one type of host cell. This means that viruses that infect eukaryotes and prokaryotes look very different and behave very different. For example, many viruses that are specific to human hosts appear to be round or displaying an isometric shape. Bacteria specific viruses, called bacteriophage, have an isometric head attached to a cylinder with legs. The varying shapes of the viruses correlate to what cell they have evolved to infect, or the environment that they most likely will reside.

Most of the viruses that infect archaea are able to infect the extremophile archaea. Archaea viruses are some of the most diverse in shape and structure of all kinds of bacteria, they also have some of the most diverse genomes, with most of the codes are for proteins that no other type of virus uses. Genome analysis has shown that archaeal viruses have little to no relationship to other types of viruses which means that they could have arisen from a different or multiple origin events.

Viruses have inhabited Earth for a very long time. This has allowed for viruses to evolve to infect every branch of life; eukaryotes, prokaryotes, and archaea. Viruses are very specific and can only infect one organism, and one type of cell.

Research has been done to attempt to classify a linear evolutionary relationship between viruses by studying the three dimensional structure of viruses. Adenoviruses (an icosahedral, dsDNA, nonenveloped virus that infects humans) and some bacteriophage have many physical similarities. That suggests that a common ancestor existed before bacteria and eukaryotes diverged. Many viruses also exhibit a “jellyroll” fold in their proteins. This protein fold is seen in 50 virus structures that are RNA viruses, DNA viruses, plant and animal viruses, and bacteria viruses. “It is, in fact, difficult to distinguish between the possibilities that this protein fold arose independently in different viral lineages at an extremely early point, or that it represents a barely discernable vestige of a non-virus progenitor that links lineages. The only evidence that many of the viral jellyrolls are homologous is that they share certain features”.

“The logical conclusion is that each of the separate lineages discussed arose from a common ancestor that existed before their host organisms diverged, some three billion years ago, to form the current domains of life”. It is unlikely “that the structural similarities reflect convergence to one of a small number of possible solutions to the problem of making a viable capsid.”

The evolution of the bacteriophage tails has been well studied by scientists. The main focus of study has been on the protein sequences that make up the tail region. One study concluded that “A single protein module has given rise to most of the proteins forming the various phage tail components as well as other needlelike assemblies”. Another study determined that horizontal gene transfer had a very large effect on the evolution of the phage tails, and that the proteins that make up the tails depends on the “host, lifestyle, and genetic composition of the phages”.

 

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How do viruses infect other host species? What is zoonosis? How do vaccines work?

Viruses sometimes jump from one species to another species, an event called zoonosis, often with deadly results because the new host population has no immunity until the entire herd is infected. Many pandemics have been the result of this phenomenon. Historically each new population that contacted contagious people suffered through the same struggle to develop herd immunity. Most human viruses originated in vertebrates like birds or mammals. In recent centuries, vaccines have been developed for a few viruses that have protected human populations by introducing what is basically a non-hereditary herd immunity.

Zoonotic viruses infect other species in the same way that viruses transfer within the same species, usually from bodily fluids. Zoonosis is very rare because viruses are very specific to a certain species. Most viruses will not survive in a new species, but if the virus is able to mutate rapidly, a new strain of the virus may be able to survive and reproduce in its new host. For this reason, zoonosis only happens when the new host is exposed to large amounts of the zoonotic virus, to ensure that enough viruses can mutate to infect the new host.

Vaccines work by introducing a strain of a virus into the body, so that the immune system creates antibodies for that strain. This helps the immune system to quickly recognize and destroy the virus if the host is to become infected. According to the CDC, there are three different types of vaccines for viruses: live, attenuated vaccines, inactivated vaccines, and subunit vaccines.

Live, Attenuated Vaccine: These vaccines contain a version of the living virus or bacteria that has been weakened so that it does not cause serious disease in people with healthy immune systems. Because live, attenuated vaccines are the closest thing to a natural infection, they are good teachers for the immune system. Examples of live, attenuated vaccines include measles, mumps, and rubella vaccine (MMR) and varicella (chickenpox) vaccine. Even though they are very effective, not everyone can receive these vaccines. Children with weakened immune systems—for example, those who are undergoing chemotherapy—cannot get live vaccines.

Inactivated Vaccines: These vaccines are made by inactivation the germ in the process of making the vaccine. This type of vaccine produces immune responses in different ways than a live vaccine, and often require multiple doses are necessary to build up or maintain immunity. The polio vaccine is an example of an inactivated vaccine.

Subunit Vaccines: Include only parts (subunits) of the virus instead of the entire germ. Side effects are less common with this type of vaccine as only the essential antigens are included. One example of this vaccine is for the pertussis or whooping cough.

 

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Viruses increase genetic diversity of offspring by horizontal gene transfer

Horizontal gene transfer is a naturally occurring process that creates more genetic diversity among prokaryotes and single celled eukaryotes. These single celled organisms reproduce by dividing which leads to genetically identical offspring other than variations due to mutations. Horizontal gene transfer enables single celled organisms to obtain new genetic material without mating.

Viruses increase the rate of horizontal gene transfer when they transfer DNA from a host cell they previously infected into new host cells. The viruses that do this have taken pieces of cellular genetic material from a previous host during their dispersion, by taking some of the cell wall with them, or through being integrated into the cellular DNA within the lysogenetic cycle. When viruses introduce new genetic material into a host cell, the host cell accepts it and adds it into its genome. This can create more diversity within the gene pool and increase or decrease beneficial adaptations to that cell and its descendants.

Horizontal gene transfer is very beneficial to single celled organisms and increases the rate of evolution and adaptation within an environment as cells are becoming better and worse suited for any particular habitat. More diversity within any population of living organisms is very beneficial for the health and prosperity of said organisms. Diversity can help ensure survival against diseases or physical disruptions in the environment. Increased genetic diversity also increases the rate of adaption and evolution. If a new combination of genes is superior to others in the population, that combination will become prominent. In this sense, viruses help foster evolution within single and multicellular organisms.

Wikipedia says that viruses are an important natural means of transferring genes between different species, which increases genetic diversity and drives evolution. It is thought viruses played a central role in early evolution, before bacteria, archaea and eukaryotes diversified, at the time of the last universal common ancestor of life on Earth. Viruses are still one of the largest reservoirs of unexplored genetic diversity on Earth. Marine bacteriophages often contain auxiliary metabolic genes, host-derived genes thought to sustain viral replication by supplementing host metabolism during viral infection. These genes can impact multiple biogeochemical cycles, including carbon, phosphorus, sulfur, and nitrogen.

 

Viruses apply selection pressures that favor the most fit individuals in a population

By selectively harming the least fit individuals in a population, viruses and other pathogens improve the fitness of future populations of a species via the principle of survival of the fittest. This applies to all species and we are no exception. We are the beneficiaries of sacrifices made by individuals over many generations that spanned millions and even billions of years. The complex and highly evolved immune system is one of many examples of the results of this process.

Viruses in general harm individuals while benefiting entire populations and communities. When a new virus enters a group of organisms, the individuals who are not able to fight the virus will get sick and possibly die. The organisms that are strong enough to fight the virus survive and continue to reproduce. This increases the strength of the population overall as the next generations have inherited either the immunity or strength against other viruses.

Although viruses have the ability to kill members of a population, these organisms most likely were not fit for their environment in the first place. In this way viruses help accelerate evolution. The weaker organisms that are less fit for their environment are not able to contribute their genes to the next generation, while the stronger organisms are. By infected and killing weak individuals, viruses selects for the strongest most fit members of the population to survive and reproduce.

Viruses may eliminate the less fit populations from ecosystems

There are many viruses that can affect eukaryotic cells and archaea. Some of the most popular viruses in the ocean have had major effects on marine organisms. In some cases, these viruses could affect humans down the line. One example of a marine virus that had a major effect on an intertidal invertebrate is the Sea star Wasting disease. Sea star wasting disease is caused by a virus and became a common illness in 2013. Its effects Sea Stars and other echinoderms and ultimately leads to their rot and death. The Sea Star population has been decimated by this disease in even our own county. The drop in Sea Star numbers has a very large effect on the rest of the marine food web. For example, Sea Stars eat mussels, so Mussels have seen a dramatic increase in numbers which has not been beneficial to the environment.

A marine virus called the rhabdovirus infects fish. The virus is similar and distantly related to the rabies virus. The symptoms of this virus include anemia, bleeding, lethargy, and a high mortality rate if their water temperature varies. This virus can ravage through hatcheries and fisheries and devastate wild populations as well. Viruses are especially dangerous in a fishery setting where the fish are living in very close proximity to each other. Rhabdovirus can be very harmful to the economy and food amounts as it can affect commonly consumed fish such as carp, perch, salmon, cod, etc.

The marine virus that infects fish is infectious salmon anemia. This virus was discovered in a fishery in Norway in 1984, and killed 80% of the fishery population. This virus is a major problem to fishers and fishery managers in the North Atlantic where much of the fish that the US consumes is from.

Marine mammals are also affected be viruses in the ocean. Seals are able to be infected by a distemper virus, similar to the disease that is found in dogs. Marine mammals are also susceptible to herpes like viruses and parvoviruses. Marine mammals are especially at risk from viruses because of their similarity to land mammals. Land viruses that are able to jump from land mammals to ocean may decimate the marine mammal community.

Viruses may keep the most fit populations from eliminating rivals

Viruses play a very important role in maintaining biodiversity and overall health in ecosystems. Through infection and subsequent death, viruses ensure that not one population of organisms becomes too abundant in an ecosystem. If all viruses disappeared, one population of organisms would take over ecosystems. This can disrupt the delicate natural balance that nature has, drastically changing the environment from plant composition to food web composition.

Viruses that attack the most fit individuals ensure that they do not completely take over the environment and change the composition of the food web. Viruses can ensure that not one population becomes to abundant which could led to the elimination of other groups of organisms.

Wikipedia says that viruses limit algal blooms. Microorganisms make up about 70% of the marine biomass. It is estimated viruses kill 20% of this biomass each day and that there are 15 times as many viruses in the oceans as there are bacteria and archaea. Viruses are the main agents responsible for the rapid destruction of harmful algal blooms, which often kill other marine life. Scientists are exploring the potential of marine cyanophages to be used to prevent or reverse eutrophication. The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms.

If phytoplankton were to die naturally or be eaten, rather than be infected with a virus, the carbon and other nutrients would either sink out of reach of other microorganisms or be moved upwards in the food web. By infecting this high number of phytoplankton everyday, viruses ensure that enough nutrients are available for microorganisms.

There is an article at https://www.tandfonline.com/doi/full/10.4161/mge.20031 that discusses hyperdiversity in viral susceptibility regions of the genetic code of bacteria. The abstract states” “Bacteria and their viruses (phages) are antagonists, yet have coexisted in nature for billions of years. Models proposed to explain the paradox of antagonistic coexistence generally reach two types of solutions: Arms race-like dynamics that lead to hosts and viruses with increasing resistance and infection ranges; and population fluctuations between diverse host and viral types due to a metabolic cost of resistance.

“Recently, we found that populations of the marine cyanobacterium, Prochlorococcus, consist of cells with extreme hypervariability in gene sequence and gene content in a viral susceptibility region of the genome. Furthermore, we found a novel cost of resistance where resistance to one set of viruses is accompanied by changes in infection dynamics by other viruses. In this combined mini-review and commentary paper we discuss these findings in the context of existing ecological, evolutionary and genetic models of host-virus coexistence. We suggest that this coexistence is governed mainly by fluctuations between microbial subpopulations with differing viral susceptibility regions and that these fluctuations are driven by both metabolic and enhanced infection costs of resistance. Furthermore, we suggest that enhanced infection leads to passive host-switching by viruses, preventing the development of hosts with universal resistance. These findings highlight the vital importance of community complexity for host-virus coexistence.”

The summary states “In summary, natural communities are complex systems whose members are constantly interacting with each other. The diversity of the players in this system are the outcome of millions of years of large-scale coevolution between viruses and their various hosts, during which host mutations have led to hypervariability in gene sequence and gene content in viral susceptibility regions of microbial genomes. Enhanced infection can serve as a driver of fluctuating selection among these diverse subpopulations which would ultimately prevent any single subpopulation from taking over the entire population. Enhanced infection also leads to passive host-switching in viruses that provides a constant supply of alternative hosts to the virus. This is especially important for viral persistence during periods of low abundances, and thus low contact rates, with preexisting susceptible hosts and likely compensates for the inherent asymmetry in the degree of phage counter-mutations. Moreover, this passive switching is also expected to prevent arms race-like super-resistant hosts from developing. These features of the system illustrate the importance of the biotic context in which an organism lives.”

Viruses increase the availability of nutrient nitrogen in oceans

Take one deep breath in…then another. You can thank viruses in the ocean for one of those breathes!

In all of the worlds oceans, phytoplankton, a microscopic organism that does photosynthesis like plants, exist near the surface. These phytoplankton produce an estimated 80% of the oxygen on Earth. In addition to phytoplankton there are other microorganisms in the ocean such as bacteria, specific heterotrophic bacteria. Heterotrophic bacteria are very small bacteria that act as recycling centers. They take in all the microscopic waste scientists call “Particulate Organic Carbon” (POC) and “Dissolved Organic Carbon” (DOC). Heterotrophic bacteria take in this waste and transform it into nutrients that other organisms can use for fuel if they eat the bacteria.

Most viruses in the ocean specifically infect heterotrophic bacteria, and phytoplankton. When one of the numerous viruses in the ocean runs into one of these bacterium, it infects the cell, and ultimately explodes the cell with all of the newly created viruses. This explosion of the bacteria cell by viruses is very important to the microorganism community in the ocean. When the bacteria explodes, all of the newly recycled nutrients it was storing gets released into the environment. These nutrients can then be used by phytoplankton to grow in size and number. By infecting and killing the bacteria, viruses help keep phytoplankton healthy and numerous, giving us more oxygen to breathe. In addition, phytoplankton take in carbon from the ocean and atmosphere as they create oxygen. If there are more phytoplankton in the ocean, more carbon can be taken out of the atmosphere, helping to decrease the greenhouse effect and global warming.

The viruses that infect phytoplankton are also very important to the ocean ecosystem. Through infection and subsequent lysing (exploding the host cell), viruses ensure the biodiversity of the phytoplankton population. If viruses did not do this, one type of phytoplankton can become too numerous and not allow other phytoplankton species to flourish. Biodiversity is very important and necessary for the health and wellbeing of an ecosystem. Biodiversity helps protect an ecosystem from disease, too much predation, large destructive events, etc.

Viruses in the ocean are very numerous and important to the health of both the oceans, and the atmosphere. If viruses in the ocean did not exist, oceans would not be able to produce as much oxygen and would not be able to take in as much harmful carbon from the atmosphere.

Viruses control the growth of phytoplankton and other life forms

Wikipedia says that marine viruses inhabit marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Viruses are small infectious agents that replicates only inside the living cells of a host organism, because they require the replication machinery of the host to replicate. They can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.

When not inside a cell or in the process of infecting a cell, viruses exist in the form of independent particles called virions. A virion contains a genome (long molecules that carry genetic information in the form of either DNA or RNA) surrounded by a capsid (a protein coat protecting the genetic material). The shapes of these virus particles range from simple helical and icosahedral forms for some virus species to more complex structures for others. Most virus species have virions that are too small to be seen with an optical microscope. The average virion is about one one-hundredth the linear size of the average bacterium.

A teaspoon of seawater typically contains about ten million marine viruses. Most of these viruses are bacteriophages which infect and destroy marine bacteria and control the growth of phytoplankton at the base of the marine food web. Bacteriophages are harmless to plants and animals, but are essential to the regulation of marine ecosystems. They supply key mechanisms for recycling ocean carbon and nutrients. In a process known as the viral shunt, organic molecules released from dead bacterial cells stimulate fresh bacterial and algal growth. In particular the breaking down of bacteria by viruses (lysis) has been shown to enhance nitrogen cycling and stimulate phytoplankton growth. Viral activity also affects the biological pump, the process which sequesters carbon in the deep ocean.

By increasing the amount of respiration in the oceans, viruses are indirectly responsible for reducing the amount of carbon dioxide in the atmosphere by approximately 3 gigatons of carbon per year

Marine microorganisms make up about 70% of the total marine biomass. It is estimated marine viruses kill 20% of this biomass every day. Viruses are the main agents responsible for the rapid destruction of harmful algal blooms which often kill other marine life. The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms. Viruses are an important natural means of transferring genes between different species, which increases genetic diversity and drives evolution. It is thought viruses played a central role in early evolution before the diversification of bacteria, archaea and eukaryotes, at the time of the last universal common ancestor of life on Earth. Viruses are still one of the largest areas of unexplored genetic diversity on Earth.

Although marine viruses have only recently been studied extensively, they are already known to hold critical roles in many ecosystem functions and cycles. Marine viruses offer a number of important ecosystem services and are essential to the regulation of marine ecosystems. Marine bacteriophages and other viruses appear to influence biogeochemical cycles globally, provide and regulate microbial biodiversity, cycle carbon through marine food webs, and are essential in preventing bacterial population explosions.

The dominant hosts for viruses in the ocean are marine microorganisms, such as bacteria. Bacteriophages are harmless to plants and animals, and are essential to the regulation of marine and freshwater ecosystems are important mortality agents of phytoplankton, the base of the food chain in aquatic environments. They infect and destroy bacteria in aquatic microbial communities, and are one of the most important mechanisms of recycling carbon and nutrient cycling in marine environments. The organic molecules released from the dead bacterial cells stimulate fresh bacterial and algal growth, in a process known as the viral shunt.

In this way, marine viruses are thought to play an important role in nutrient cycles by increasing the efficiency of the biological pump. Viruses cause lysis of living cells, that is, they break the cell membranes down. This releases compounds such as amino acids and nucleic acids, which tend to be recycled near the surface.

What if all viruses disappeared?

While living through a pandemic, such as the current COVID-19 crisis, it is easy for people to wish for all viruses to disappear. If this could happen, it would solve some problems such as the current COVID-19 crisis, and other deadly viral infections. However, if all viruses one day disappeared, many deadly problems would arise.

One of the most prominent issues that would arise if viruses were to go away would be that the amount of carbon dioxide in the atmosphere would increase, and the amount of oxygen would decrease. Viruses in the ocean are vital to the process of taking in carbon out of the atmosphere and producing oxygen, through their assisting the health of phytoplankton populations. The increase of carbon dioxide in the atmosphere would cause the temperature of the air to increase dramatically. This can cause dramatic weather events such as large storms or droughts that can prove dangerous and deadly to humans and their lively hoods. The decrease in oxygen production causes a blatant issue as humans would lose one of their main sources of breathable air. Viruses in the ocean also control the abundance of bacteria in the ocean. If no viruses existed, the ocean would fill with bacteria most likely killing all of the other organisms in the ocean.

Viruses also play a very important role in maintaining biodiversity and overall health in ecosystems. Through infection and subsequent death, viruses ensure that not one population of organisms becomes too abundant in an ecosystem. If all viruses disappeared, one population of organisms would take over ecosystems. This can disrupt the delicate natural balance that nature has, drastically changing the environment from plant composition to food web composition.

Viruses are also important to maintaining the strength and versatility of the human immune system. If the human immune system were to not be exposed to different viruses daily, it could lose resilience and immunity, leading to more sickness.

Although it seems like a great idea to eliminate all viruses on Earth, it could be deadly to all life forms. Viruses help maintain balanced and intricate systems all over the planet, removing them would be detrimental. With no viruses, we wouldn’t get the flu, or COVID-19, but we would also not be able to breathe a normal amount of oxygen, be exposed to extreme weather, and lose important food sources. In conclusion, if anyone had the power to make all viruses disappear, they shouldn’t do it.

 

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The viral shunt affects the biological pump

The viral shunt is a process that is done in the ocean between bacteriophages and heterotrophic bacteria. “It prevents marine microbial particulate organic matter from migrating up the trophic levels by recycling them into dissolved organic matter which can be easily taken up by other organisms”. The viral shunt is an important aspect to both marine food webs and the overall health of the ocean environment.

Heterotrophic bacteria are able to take in nutrients from the environment that are in an organic state and are unable to be taken up by other organisms. The bacteria can then fix these nutrients into a form that is usable to organism that are higher up on the food web.

Viruses in the ocean are mainly bacteriophages, and infect these heterotrophic bacteria, eventually lysing them. When the bacteria are lysed, the nutrients that they have fixed is also expelled into the ocean, allowing the nutrients to be returned back to the microbial community rather than rising up the food chain. This is beneficial for the microbial community as the ocean is supported by Phyto and zoo plankton, and would not be as healthy without a large number of them. This also supports the idea that an ecosystem can support a large number of smaller organisms, but it cannot support a large number of larger organisms.

Viruses attack and kill about half of the population of heterotrophic bacteria and phytoplankton populations a day. Thus, keeping the populations in check in terms of size and diversity. This can also be an argument that viruses are continuously aiding and helping in the evolution of bacteria and phytoplankton. Perhaps Heterotrophic bacteria and phytoplankton looked very different before and were more susceptible to being destroyed by a virus.

Excerpts from Wikipedia:

The viral shunt pathway facilitates the flow of dissolved organic matter (DOM) and particulate organic matter (POM) through the marine food web Connections between the different compartments of the living (bacteria/viruses and phytoplankton/zooplankton) and the nonliving (DOM/POM and inorganic matter) environment.

Viral activity also enhances the ability of the biological pump to sequester carbon in the deep ocean. Lysis of microorganisms releases more indigestible carbon-rich material like that found in cell walls, which is likely exported to deeper waters. Thus, the material that is exported to deeper waters by the viral shunt is probably more carbon rich than the material from which it was derived. By increasing the amount of respiration in the oceans, viruses are indirectly responsible for reducing the amount of carbon dioxide in the atmosphere by about three gigatons of carbon per year. Lysis of bacteria by viruses has been shown to also enhance nitrogen cycling and stimulate phytoplankton growth.

The viral shunt pathway is a mechanism that prevents (prokaryotic and eukaryotic) marine microbial particulate organic matter (POM) from migrating up trophic levels by recycling them into dissolved organic matter (DOM), which can be readily taken up by microorganisms.

Viral shunting helps maintain diversity within the microbial ecosystem by preventing a single species of marine microbe from dominating the micro-environment. The DOM recycled by the viral shunt pathway is comparable to the amount generated by the other main sources of marine DOM.

Viruses are the most abundant biological entity in marine environments. Most of these viruses are bacteriophages infecting heterotrophic bacteria and cyanophages infecting cyanobacteria. Viruses easily infect microorganisms in the microbial loop due to their relative abundance compared to microbes. Prokaryotic and eukaryotic mortality contribute to carbon nutrient recycling through cell lysis.

There is evidence as well of nitrogen (specifically ammonium) regeneration. This nutrient recycling helps stimulates microbial growth. As much as 25% of the primary production from phytoplankton in the global oceans may be recycled within the microbial loop through viral shunting.

Viruses mitigate global climate change

Carbon in the Earth’s atmosphere has a large effect on the global climate. Global warming is caused by the greenhouse effect; gasses such as carbon dioxide, methane, and water vapor in the trap the sun’s rays and heat in the atmosphere causing a general rise in temperature. Increasing the temperature of the planet is very dangerous, it causes changes in climate and weather patterns which can cause ice melts, sea water warming, ocean acidification, droughts, etc.

Viruses in the ocean have been shown to influence the carbon cycle and thus the climate, in a positive way. Viruses in the ocean affect the health and population of phytoplankton through releasing nutrients in bacteria into the ecosystem. By releasing the nutrients for phytoplankton to use, viruses can increase the health and abundance of phytoplankton in the ocean. Phytoplankton are very important organisms to the wellbeing of Earth. Along with creating 80% of the oxygen on Earth, phytoplankton take in a large amount of carbon dioxide from the atmosphere.

In a process that scientists call the Biological Pump, carbon (in the form of carbon dioxide) is taken from the atmosphere by phytoplankton, and then moves through the food chain as an organism eats the phytoplankton and then gets eaten itself. The biological pump ends with the carbon that is now stored in an organism’s body (fish, whales, or even phytoplankton themselves), sinks to the bottom of the ocean and is stored in sediment. The ocean is called a “carbon sink” because of its great ability to store carbon through the biological pump.

The high efficiency of the biological pump is important in mitigating global warming. Viruses improve the effectiveness of the  biological pump. Marine viruses increase the amount of phytoplankton and bacteria that affect the amount of carbon being dissolved in the ocean and entering the biological pump. Viruses indirectly decrease the amount of carbon in the atmosphere, decreasing the rate of warming due to the greenhouse effect. Thus, viruses indirectly have power over the climate. Less viruses could mean more carbon in the atmosphere, leading to more heat in the atmosphere which could cause more large storms such as hurricanes or droughts.

Viruses have a very important part of the carbon cycle through their position in the ocean’s biological pump. Because viruses generally increase the health and abundance of phytoplankton, they decrease the amount of carbon dioxide in the atmosphere, helping to decrease the greenhouse effect.

These paragraphs are phrased excerpts from https://academic.oup.com/femsre/article-abstract/35/6/993/524824:

Viruses play a pivotal role in the functioning of both pelagic and benthic ecosystems, influencing microbial food webs, controlling prokaryotic diversity and impacting biogeochemical cycles.

It is unclear whether viruses, under the present scenarios of climate change, will ultimately stabilize or destabilize the dynamics of the living components of ecosystems and their biogeochemical cycles. Therefore, we cannot yet predict whether the viruses will exacerbate or smooth the impact of climate change on marine ecosystems. The effect of rising surface water temperatures on viruses will be significant, influencing both the metabolism and growth efficiency of the prokaryotes and altering the viral life cycles.

Different effects will be observed at different latitudes and in different oceanic regions. There is evidence that higher temperature will promote the viral component at high latitudes and depress it at the tropics. The scenario of freshening at the poles will likely increase the input and spread of freshwater groups of viruses and bacteria into marine systems, along with increasing opportunity for crossing over of marine and freshwater taxa.

Marine viruses can influence the metabolic balance of heterotrophic prokaryotes, inducing shifts in pelagic ecosystems function. However, it is unclear whether the viral shunt will ultimately have positive or negative effects on the efficiency of the biological pump, and consequently, the feedback effects of marine ecosystems on climate. The role of viruses on the carbon export to the ocean interior may be crucial.

Viruses have the potential to interact with the climate through their contribution to the marine biogenic particles of the aerosol and by contributing to the release of dimethyl sulfide through the lysis of their autotrophic hosts. The oxygen minimum zones are predicted to expand in the future ocean because of climate change, with important consequences on biogeochemical cycling of nitrogen and phosphorus and on the distribution of organisms. Because eukaryotic herbivores and bacterivores are more sensitive than prokaryotes to the reduction in oxygen levels, virus-induced mortality of prokaryotes may increase at the expense of protists and other bacterivores. Expanding oxygen minimum zones will also lead to an increase in the frequency of anoxic sediments and thus potentially the global role of viruses in benthic prokaryotic dynamics.

The effects of ocean acidification on marine viruses are uncertain, but we can anticipate that the most dramatic changes will be due to the effects of pH on the host organisms that the viruses rely on bacteria, archaea, protists and metazoa, which are highly pH dependent. Moreover, because some key metabolic processes of the microbial communities are highly sensitive (and inhibited) by even small decreases in the pH of the medium, ocean acidification may have a profound influence on the overall functioning of the microbial communities and on virus–host interactions. Studies suggest that marine viruses will be significantly influenced by climate change and that viruses could influence processes contributing to climate change.

Viruses mitigate ocean acidification

Ocean acidification is one of the most important consequences of climate change. The pH of the ocean decreases or becomes more acidic when more atmospheric carbon enters the ocean. High levels of carbon are being produced daily through emissions from factories, cars, etc. Increases in ocean acidity are detrimental to all oceanic ecosystems. The low pH decreases the strength of the shells of organisms such as snails and crabs. The low pH also creates a stressful chemical environment that can disrupt oxygen levels and chemical signals of animals.

Marine viruses indirectly increase the amount of carbon being sequestered by phytoplankton in a form that is not harmful to the pH or chemical balance of the ocean. This mitigates the solution of atmospheric carbon in the ocean that disrupts habitats. A higher number of viruses leads to a higher number of healthy phytoplankton.

We previously discussed the fact that viruses enhance the biodiversity of marine ecosystems by keeping the most fit populations from eliminating rivals, increasing the availability of nutrient nitrogen in oceans, and controlling the growth of phytoplankton and other life forms. It turns out that viruses are important because the biodiversity that they enhance mitigates ocean acidification. The following three paragraphs are paraphrased excerpts from https://www.nature.com/articles/s41598-020-59886-4.pdf:

A high biodiversity mitigates the impact of ocean acidification on hard-bottom ecosystems. Biodiversity loss and climate change simultaneously threaten marine ecosystems, yet their interactions remain largely unknown. Ocean acidification severely affects a wide variety of marine organisms and recent studies have predicted major impacts at the pH conditions expected for 2100.

The interdependence between biodiversity and ecosystem functioning is well established. Scientists suspect that the species’ response to ocean acidification depends on the biodiversity of the natural multispecies assemblages in which they live. Scientists have investigated the impact of acidification on key habitat-forming organisms (including corals, sponges and macroalgae) and associated microbes in hard-bottom assemblages characterized by different biodiversity levels. High biodiversity appears to lessen the impact of acidification on otherwise highly vulnerable key organisms by 50 to 90% or more, depending on the species.

Higher biodiversity can be associated with higher availability of food resources and healthy microbe-host associations, overall increasing host resistance to acidification, while contrasting harmful outbreaks of opportunistic microbes. Given the climate change scenarios predicted for the future, biodiversity conservation of hard-bottom ecosystems is fundamental for mitigating the impacts of ocean acidification.

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virus bacteria NetLogo model description

WHAT IS IT?

This toy model explores the stability of marine virus-bacteria ecosystems. Such a system is called unstable if it tends to result in extinction for one or more species involved. In contrast, a system is stable if it tends to maintain itself over time, despite fluctuations in population sizes.

The current model does not allow any agents to evolve and our bacteria do not have an immune system. They always die when infected. Bacteria are not contagious. They lyse and the resulting viruses drift randomly in a sea of bacteria until they infect a bacterium. The virus hatch rate is one less than the number resulting from an infection because the model allows the infecting virus to continue to drift.

So far I have not found any initial conditions or parameters that lead to stable diverse populations of bacteria. I think this is a fundamental feature of the current model rather than unfortunate selection of parameters. I think the reason is that bacteria do not produce diverse offspring and do not evolve or have immune systems and because all infected bacteria die and spread viruses.

The cases I have run have one of three outcomes. Either the less fit goes extinct or the the viruses kill the winner or all bacteria go extinct. Outcomes are not always predictable because of the built in random factors. Along the way, bacteria experience repeated cycles of exponential growth followed by near extinction population crashes. The model has a user-specified maximum population condition which limits growth and plays a major role in the course of the outcome of each case.

Any extinction event is a failure for the viruses as well because they too go extinct.

In a model that permits diverse offspring, the population declines may be stabilized as natural selection favors virus-resistant offspring or offspring with other stabilizing parameters. Like nature itself a more sophisticated model may find the right parameters for populations to have diversity and relative stability.

The model is not complete yet and neither is this information tab. If there are any bugs in the model, they are most likely associated with the sequence of instructions in the code or the conditional if statements.

HOW IT WORKS

Bacteria and viruses move randomly through the ocean. They bounce off the surface. They die if they enter the gray bottom zone. The ocean wraps horizontally. This world is 100 x 100 patches.

Nutrients are assumed to be uniformly distributed but bacteria stop reproducing when the total maxes out due to an unspecified environmental limit. There are user-specified rates that a bacterium will multiply or die on any tick. There is also a user-specified rate that a virus will die on any tick. When the bacteria population is maxed out, it can reproduce again each time one of them dies.

A bacterium also dies if a virus lands on its patch of ocean after the virus multiplies. The global variable fatalities counts how many times this has happened.

In the current model, neither the bacteria nor the viruses are evolving. Also bacteria do not survive infections; unlike multicellular organisms, they cannot be carriers of infection.

When the viruscolors switch is off, the colors do not mean anything. When it is switched on, red viruses only infect green bacteria and yellow viruses only infect blue bacteria.

Statistician George Box said, “All models are wrong, but some are useful”. How “useful” is this model? How “wrong” is it?

CURRENT MODEL INPUTS

The current inputs are:

initial-viruses 10________random red or yellow
hatchviruses 3_________per infection
virusdeathrate 20_______random per 1000
initial-bacteria 500______random green or blue based on ratio input
bacteriahatchrate 50____random per 1000
bacteriadeathrate 1_____random per 1000
greenblueratio 3_______random
maxbacteria 1000
step 3_______________random
viruscolors on_________red viruses infect green bacteria yellow viruses infect blue bacteria
message off
newviruses off
click “setup” and then either “GO” or “GO ten”
tick speed normal or much faster

HOW TO USE IT

1. Adjust the inputs.
2. Adjust the slider parameters (see below) and input values, or use the default settings.
3. Press the SETUP button.
4. Press the GO button to begin the simulation. Press GO again to stop it at the end of the current tick. To run the model for ten ticks, press the “GO ten” button.
5. Look at the monitors to see the current population sizes
6. Look at the POPULATIONS plot to watch the populations fluctuate over time
7. Watch the model run for several minutes to see what happens.
8. Adjust tick speed slider at the top to slow things down or speed things up.

Notice that the plot autoscales over time as needed. The second plot shows the ratio of green bacteria to blue bacteria. In the absence of viruses, the blue and green bacteria populations do not converge to the user-specified greenblueratio value. The higher hatch rate of green will win each time.

Notice that the behavior changes abruptly when the total number of bacteria maxes out.

In the presence of viruses, bacteria experience rapid blooms or surges followed by population crashes. With viruscolors switched off and a high virus death rate, the green bacteria have a better chance of survival, but sometimes all of the bacteria go extinct. The deeper the crash, the more likely the viruses will die out before the bacteria get crowded again.

With viruscolors on, there are wild polulation fluctuations, but blue bacteria tend to survive due to social distancing since the green help keep their numbers down.

Parameters:

The world has 100 x 100 patches. It wraps horizontally so that turtles that disappear to either side enter on the other side. Turtles that are near the bottom die. Turtles near the upper surface bounce back. Turtles take steps in random directions on each tick.Viruses and bacteria are different breeds of turtle. They only hatch their own color. When the viruscolors switch is on, red viruses only infect green bacteria and yellow viruses only infect blue viruses. Bacteria always die when infected and viruses always hatch the same number of offspring in each infection.

There are ten monitors to show the populations of red and yellow viruses, green and blue bacteria, all bacteria, bacteria created, viruses created, infections, other deaths, and current green blue ratio. Timer (seconds) and ticks are also monitored. The populations plot displays the population of viruses/10 and bacteria over time.

The green blue ratio is an integer that determines the green bacteria hatch rate relative to the blue bacteria hatch rate. A ratio of 3 means that a green bacteria is three times as likely to hatch another green bacteria randomly as a blue is to hatch a blue.

If there are no viruses left, the model run stops if the message switch is on.
You can introduce new viruses randomly whenever the newviruses switch is on.

THINGS TO NOTICE

When running the model, watch as the populations fluctuate. Notice the interesting spatial and temporal patterns. Notice that increases and decreases in the sizes of each population are related. In what way are they related? What eventually happens?

What are you learning about the effect of viruses on bacteria and vice versa?

On average, how does the ratio of viruses to bacteria compare to the initial ratio?
What happens when a population of bacteria surges?
What happens when a population of viruses surges?

With viruscolors switched off, the two populations of bacteria and the two populations of viruses are identical and have no advantages over the other. Keep a record of which colors go extinct on each run and see what you learn.

Why do you suppose that some variations of the model might be stable while others are not?

THINGS TO TRY

Case 1 - zero viruses
Case 2 - viruses but viruscolor off
Case 3 - viruses and viruscolor on
Case 4 - try 2000 initial bacteria
Case 5 - if viruses go extinct turn newviruses on - see who survives and how well they do

Try adjusting the parameters under various settings. How sensitive is the stability of the model to the particular parameters?

Can you find any parameters that generate a stable ecosystem in the model variation?

Notice that under stable settings, the populations tend to fluctuate at a predictable pace. Can you find any parameters that will speed this up or slow it down?

EXTENDING THE MODEL

Try changing the reproduction and death rates. What would happen if reproduction depended on _________ rather than being determined by a fixed probability?

What would happen if populations evolved? Suppose offspring had a diversity of properties like movement, multiplication, death rate? What if we only started with one color virus and one color bacteria, but evolving offspring varied in color?

What if our bacteria had an immune system?

 

;virus bacteria NetLogo model by Bob Field 2020-0823
breed [bacteria bacterium]   breed [viruses virus]

globals [infections otherdeaths]

to setup
  clear-all
  ask patches [set pcolor gray]
  ask patches [if pycor > -45 [set pcolor blue + 3]]
  create-bacteria initial-bacteria [set shape "circle" set size 2 setxy random-xcor random-ycor ifelse random 2 = 0 [set color green] [set color blue]]
  create-viruses initial-viruses [set shape "bug" set size 2 setxy random-xcor random-ycor ifelse random 2 = 0 [set color red] [set color yellow]]
  set infections 0 set otherdeaths 0
  reset-ticks   reset-timer
end

to go
  tick
  ask turtles [if ycor > 48 [set ycor 48]]
  ask viruses [set heading (random 360) fd random step if ycor < -45 [die]]
  ask bacteria [set heading (random 360) fd random step if ycor < -45 [set otherdeaths otherdeaths + 1 die]]
  ask bacteria [if (count bacteria < maxbacteria and random 1000 < bacteriahatchrate) [ifelse random (greenblueratio + 1) = 0 [if color = blue [hatch 1]] [if color = green [hatch 1]]]]
  ask bacteria [set heading random 360 fd 1]
  if viruscolors = true [ask viruses with [color = yellow] [if any? bacteria-here with [color = blue] [hatch hatchviruses set infections infections + 1]]]
  if viruscolors = true [ask viruses with [color = red] [if any? bacteria-here with [color = green] [hatch hatchviruses set infections infections + 1]]]
  if viruscolors = true [ask bacteria with [color = blue] [if any? viruses-here with [color = yellow] [die]]]
  if viruscolors = true [ask bacteria with [color = green] [if any? viruses-here with [color = red] [die]]]
  if viruscolors = false [ask viruses [if any? bacteria-here [hatch hatchviruses set infections infections + 1]] ask bacteria [if any? viruses-here [die]]]
  ask viruses [if random 1000 < virusdeathrate [die]]

  ask bacteria [if random 1000 < bacteriadeathrate [die set otherdeaths otherdeaths + 1]]
  if message = true [if not any? viruses [user-message "viruses extinct - switch message off"] if not any? bacteria [user-message "bacteria extinct"]]
  if not any? turtles [stop]
  if count turtles > 10000 [stop]
  if random 1000 < 1 and newviruses = true [create-viruses 1 [set shape "bug" set size 2 setxy random-xcor random-ycor ifelse random 2 = 0 [set color red] [set color yellow]]]
end

 

Eukaryotic cells are much larger and more complex than prokaryotic cells

Cells are the basic unit of structure and life on Earth. They are often referred to as the building blocks of life because all living things are made of cells. Cell theory is the commonly accepted and believed theory that all organisms come from cells, and that cells are the fundamental unit of structure and function in all living organisms, and that cells come from cells.

Cells generally have three main features: a stable and semi-permeable membrane, genetic material in the form of RNA or DNA which can be passed on to new cells and controls cellular behavior and function; and energy transformation via metabolic pathways which enables growth, self-maintenance and reproduction.

There are two main types of cells: prokaryotic and eukaryotic. Prokaryotic cells do not contain a nucleolus to contain its genetic material and is also lacking some of the other organelles that eukaryotic cells have. Prokaryotic cells are single celled organisms while eukaryotic cells can aggregate to create multicellular organisms

A prokaryotic cell is simpler than the eukaryotic cell and has three regions. A plasma membrane that surrounds the cell, which is also surrounded by a cell wall. Some bacteria may have a third layer that is called a capsule. The outside of prokaryotic cells can have flagella and pili which are used for movement and communication and are made out of proteins the cytoplasmic region is within the cell and holds the free-floating genetic material and other materials such as ribosomes. Prokaryotes are also able to have extrachromosomal DNA called plasmids. Plasmids are circular and are used to exchange information with other prokaryotic cells.

Eukaryotic cells are what make up plants, animals, archaea, fungi, etc. They are about 15x larger then prokaryotic cells and can be 1000x larger in volume. Cells today are made up of numerous organelles which each have a function in the creation of proteins, as well as the nucleolus, in which genetic material is held. The organelles sit in cytoplasm which is surrounded by a cell membrane. Eukaryotes have compartmentalization, and the presence of membrane bound organelles which makes them different from prokaryotes. Eukaryotic cells are also more diverse and differ depending on their location or specification, or what type of eukaryotic cell that they are.

Cells emerged at least 3.5 billion years ago and were much simpler and more permeable then the cells that we are made up of in current times.

One of the largest questions when it comes to the origin and evolution of cells is the creation and diversification of the semi-permeable phospholipid bilayer in which all cell membranes are made up of. Early cells most likely only had one layer of lipids instead of the current bilayer that cells have today. Phospholipids are only formed from living things, but fatty acids such as lipids can be formed in the environment through chemical reactions, which could explain an origin of the first cell’s membrane.

The first cells have been nicknamed “protocell” which is defined as a self-organized, endogenously ordered, spherical collection of lipids proposed as a stepping stone of life. These first cells have been theorized to arise from deep sea hydrothermal vents, or inland condensed and cooled geothermal vapor pools, based on the chemicals and nutrients available in these places. Protocells would not have been surrounded by a cell membrane of phospholipids, but more likely a membrane of easily made or found fatty acids (monolayers or bilayers). Protocells would have contained self-replicating RNA (which would have included an RNA replicas) inside of the membrane. Protocells were very simple and basic cells that looked and acted like the modern cell, they were capable of storing information, reproduction, and exchanging this information with other cells.

Archaea

Archaea are prokaryotic single cell organisms that make up the third branch of life beside bacteria and eukaryotes. They are a separate branch due to differences in their DNA in their ribosomes. Although they are single celled and seemingly simple, archaea have many similarities to eukaryotic cells in their genes and metabolic pathways. Archaea are generally more similar to eukaryotes then to the bacteria that they physically resemble in size and complexity. It is hypothesized that archaea and eukaryotes share a common ancestor more recent than Archaea and bacteria.

Like bacteria, archaea reproduce asexually using binary fission. The first archaea that were discovered were a type of archaea called “extremophiles” which are capable to live in extreme conditions such as high or low heat, high or low pH, etc.

Since their discovery, archaea have been found in every environment and are one of the most  abundant living organisms on the planet. Humans have a large composition of archaea within our body, especially our digestive system, mouth, and skin.

Archaea are involved in many important processes on earth including carbon fixation, nitrogen cycling, organic compound turnover, etc.

 

How do bacteria and other single-celled organisms fight viruses?

The ability to fight viral infections and survive is essential to evolution and the survival of all living species. The immune response to viruses varies from organism to organism, but all living things appear to have some method of fighting viruses. The strength and ability of an organism’s immune system depends on its evolutionary history, and its individual needs.

As a rule of thumb, immune response increases in complexity and strength as the organism increases with complexity. Immune systems have been vital to survive life on Earth and the same methods of immunity are seen throughout different organisms on Earth. The most basic step of having an immune system is being able to recognize viruses or viral DNA. The next step is to be able to pass down this knowledge to the organisms’ offspring.

There are two different types of immune systems: innate and adaptive. Innate immune systems are systems that have the same response, regardless of the pathogen. Adaptive immune systems are systems that learn and remember certain pathogens, such as specific viral genomes.

Bacteria are among the simplest living organisms on the planet. They have a multi-step immune system. Bacterial cells have both an innate and adaptive immune system. Bacterial cells and other prokaryotes use systems called CRISPR-CAS systems to identify viral genetic material and cut that sequence out of the cellular DNA. CRISPR-CAS has the ability to store and remember viral genetic sequences to identify them in the future.

Single celled organisms are the only living things to have CRISPR mechanisms. Eukaryotes, or multicellular organisms do not show this immune defense system. Scientists do not know whether CRISPR evolved in single celled organisms after multicellular organisms evolved and split, or if multicellular organisms once had this mechanisms and devolved it.

To paraphrase https://www.realclearscience.com/blog/2012/09/bacteria-have-immune-systems-too.html:

Even single celled bacteria have immune systems. An immunological protein system called CAS may recognize the viral DNA as foreign. When it does, the bacterium will snip out a piece of the viral DNA and then incorporate it into its own genome. This DNA sequence then serves as something of a bar code, allowing the bacterium to recognize this DNA as dangerous and to pass on this information to its offspring.

The viral DNA bar code is referred to as a spacer. The bacterium has a unique location (called a locus) in its genome where it accumulates many different bar codes from the many different viruses it has encountered. The DNA is then transcribed to produce non-coding (which means it doesn't encode protein) RNA which contains the same bar code information as the DNA.

Then, other proteins in the CAS system pick up this RNA and use it to identify foreign, invading DNA. The next time a bacterium (or one of its offspring) encounters the exact same foreign DNA, it will match the RNA bar code, and the bacterium will know that this DNA is dangerous and must be destroyed immediately. The virus is toast before it even has a chance to inflict any damage on the bacterium!

 

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How do multicellular organisms (algae, fungi, plants, and animals) fight viruses?

 

this section is incomplete and needs more detail

Bacteria are thought to be one of the first living organisms that inhabited the planet. Their immune system appears to be the basis for every other living organism’s immune response. Algae and Fungi, other Prokaryotic cells use proteins within their cell to recognize self and non-self. This is the most basic function of an immune system. The topic of algae and fungi virus immunity is a fairly new field. Many researchers are currently researching the anti-viral properties of both in the aid of the human immune system.

Interestingly enough, fungi are more closely related to animals than they are plants. Their latest common ancestor was a single cellular organism called a protist. This could mean that a fungi’s immune response is looks more like an animal’s response, rather then a plant.

Multi-cellular plants are very simple in comparison to animals but have a long evolutionary history. The plant immune system is very simple and resembles their bacterial ancestor rather than animals. Components of the plant immune system could be  both adaptive and innate. Plants do have the evolved ability to identify self vs. non-self and have more complex methods of fighting off viruses. The most common method of immunity used by plants is through RNA silencing. RNA silencing is an evolved trait in eukaryotes, which uses non-coding RNA to silence viral genetic material. Plants can recognize when genetic code is not plant, like viral genetic material, and begin to make sure that the genetic code is not expressed. If viral genetic material is expressed, plant cells would create more viruses. By ensuring that the viral genetic material is not expressed, the plant is stopping the reproduction and thus infection of a virus.

Invertebrates such as marine Sponges, insects, etc., have an immune response which is more developed than the previous organisms, but not as complex as vertebrate immune systems. Invertebrates again could have an adaptive and, or an  innate immune system which is triggered by different pathogens, and at different stages of infection. Many invertebrates have phagocytes which are innate, pathogen engulfing cells. These phagocytes that evolved with invertebrates are also a significant part of the vertebrate immune system. More commonly than not, invertebrates have a more innate response, using protective skin layers and behaviors that protect against potential infections. Invertebrates are very diverse which leads to a great diversity in immune response. This can be due to convergent evolution, or the die off of certain immune traits that did not suit certain invertebrates.

Vertebrates, the most complex of all living organisms have the most complex and evolutionary significant immune system. Vertebrate immune systems have both innate and adaptive immunity, with its adaptive immune capability being incredibly strong. Adaptive immunity is better at fighting viruses and can learn at a high rate to ensure survival. This is why we see more adaptive responses with more complex organisms, such as invertebrates and vertebrates. Humans, vertebrate animals, have the most complex immune system on Earth.

 

 

 

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How do humans fight viruses? What is the history of pandemics?

Have you ever come down with the flu? Most likely you had bad symptoms such as a fever, headache, nausea, but felt better in about four days. The reason that humans are able to fight viruses that cause these symptoms is because of a highly intricate and evolved immune system that is common to many animals, particularly mammals.

How does the human immune system differ from other animals?

The human immune system has evolved because of ancestral and past viral infections. The first defense against viruses is the largest organ of the body, the skin. Skin creates a barrier so that there are few places that a virus can actually enter the human body; the eyes, mouth, nose, and open wounds. When a virus enters the body, it will begin to infect cells.

Humans fight viruses through the use of scientifically proven tools such as sanitizers, social distancing, face coverings, medicines, and vaccines (as discussed in the previous section). If infected by a virus, there are few drugs that can be taken to eliminate the infection. The few drugs that have been invented are for very specific viruses, not your everyday flu. The immune system is the only line of defense between humans and the many viruses of the world.

Humans use many different methods of denaturation to fight against viruses. One way is to heat food to high temperatures to kill viruses. Another common way to destroy viruses is with hand sanitizer, cleaning sprays, or wipes. Hand sanitizer contains an alcohol called ethanol. Exposure of a virus to low pH or acidic substance like alcohol denatures their proteins rendering the virus inactive. Cleaning sprays like bleach or Clorox wipes can either be very basic or very acidic, which have the same destructive result to a virus.

Unlike bacterial infections, viral infections are very difficult to destroy using medicines. However antiviral medications have been created to aid in the destruction of viral infections and to help minimize the symptoms. Antiviral medications work by stopping the virus from replicating at various stages of the viral replication cycle. The medication can stop enough viral replication, allowing the human immune system to be able to destroy the pathogens. Because of the nature of viruses, their complexity and their ability to mutate rapidly, only a handful of antiviral medications are available. These medications are created to treat very specific strains of viruses. Currently, antiviral medications are available for HIV, herpes, hepatitis B and C, and influenza A and B. Antiviral medications are also difficult to create because the drug must be able to destroy or hinder the virus useless, all while having little to no effect on the host cell, or the overall health of the host.

Wikipedia says that monoclonal antibody therapy is a form of immunotherapy that uses monoclonal antibodies (mAb) to bind monospecifically to certain cells or proteins. The objective of this treatment is to stimulate the patient's immune system to attack those cells. Alternatively, in radioimmunotherapy a radioactive dose localizes a target cell line, delivering lethal chemical doses. Immune checkpoint therapy uses antibodies to bind molecules involved in T-cell regulation to remove inhibitory pathways that block T-cell responses.

In the known history of humans on Earth, there have been numerous viral pandemics that have plagued societies. One of the deadliest viral pandemics was the Spanish Influenza which killed 17-100 million people worldwide from 1918 to 1920. Viral pandemics, such as COVID-19, happen because a new virus is introduced into a population that has no former immunity to it. Because society has no immunity to this virus, it is very easy for it to thrive and reproduce rapidly.

  

Pandemics also occur when the virus is able to mutate rapidly. Rapid mutation allows for it to infect more and more hosts. Mutations also make it harder to create a therapy that works for all infected hosts. The best way to stop viral pandemics is to slow the spread, thus not allowing the virus to reproduce. This can be done by quarantining as much as you can and wearing a face covering when in public.

Here are three YouTube videos that provide more information:

https://www.youtube.com/watch?v=UG8YbNbdaco

https://www.youtube.com/watch?v=Qi0edf_nJDo

https://www.youtube.com/watch?v=_uL0ZgV6POc

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Wikipedia articles

 

We uploaded PDFs of these articles so that you can download them by clicking on these links and viewing on printable pages. The Wikipedia website may have updated version of the articles.

Antibody - wiki

Apoptosis - wiki

Archaea - wiki

Auxiliary_metabolic_genes - wiki

B_cell - wiki

Biogeochemical_cycle - wiki

Biological_pump - wiki

Competitive_exclusion_principle - wiki

Diffusion - wiki

Dimethyl_sulfide - wiki

Ecosystem_services - wiki

Endogenous_retrovirus - wiki

Escherichia_virus_CC31 - wiki

Eukaryote - wiki

Geochemical_cycle - wiki

Immune_system - wiki

Lymph - wiki

Lymphocyte - wiki

Lysis - wiki

Lysogenic_cycle - wiki

Lytic_cycle - wiki

Marine_viruses - wiki

Microbial_loop - wiki

Monoclonal_antibody - wiki

Natural_killer_cell - wiki

Natural_killer_T_cell - wiki

Osmotic_pressure - wiki

Oxygen_minimum_zone - wiki

Paradox_of_the_plankton - wiki

Phagocyte - wiki

Phagocytosis - wiki

Platelet - wiki

Red_blood_cell - wiki

Retrotransposon - wiki

Retrovirus - wiki

RNA_world - wiki

Species - wiki

Survival_of_the_fittest - wiki

T_cell - wiki

T-cell_receptor - wiki

Transposable_element - wiki

Unified_neutral_theory_of_biodiversity - wiki

Viral_envelope - wiki

Viral_shunt - wiki

Viroid - wiki

Virus - wiki

White_blood_cell - wiki

Zoonosis - wiki

 

OpenStax free textbooks and other resources

 

https://openstax.org

https://openstax.org/subjects/science

https://openstax.org/details/books/biology-2e

https://openstax.org/details/books/concepts-biology

https://openstax.org/details/books/microbiology

more videos

 

this accordion is under construction but here are some links for now:

Some YouTube searches:

https://www.youtube.com/results?search_query=evolution+virus

https://www.youtube.com/results?search_query=virus+placenta+evolution

 

I watched some of these - the placenta story is particularly interesting because a fertilized egg is like an invading particle:

https://www.youtube.com/watch?v=CDA1ISk0rlI

https://www.youtube.com/watch?v=nWuV6PVKv1A

https://www.youtube.com/watch?v=FmX8au0xGlY

https://www.youtube.com/watch?v=ZF9bjAfYm_s

https://www.youtube.com/watch?v=bTLD6Nki92A

https://www.youtube.com/watch?v=Opdp5L1bVAY