This is a longer version of a lecture that I delivered on Zoom to the Agnostics Group in Melbourne, Australia on Saturday 13 November, 2021.

VIRUSES, BACTERIA, ARCHAEONS, and EUKARYOTES

Our planet Earth is inhabited by viruses, bacteria, archaeons, and eukaryotes. These inhabitants comprise a tiny proportion of Earth’s total mass, but they pervade the land, the sea, and the atmosphere. There are trillions of some kinds of them almost everywhere. We study them scientifically and classify the ones we know about.

Bacteria and archaeons are called prokaryotes. We, ourselves, constitute a small proportion of the eukaryotes. Prokaryotes and eukaryotes are organisms. Viruses are just viruses.

All of these entities come in a multitude of sizes, shapes, and compositions. All rely on DNA and/or RNA for their existence and operation. And they are all continually evolving.

They have continually transformed the surface and atmosphere of the earth. This started with the bacteria that produced oxygen.  This decreased the atmospheric carbon dioxide, and changed the chemistry of the crust. Some oxygen became ozone. Further transformation has continued  to today, where humanity keeps disrupting the biota and the terrain.

Viruses, bacteria, and archaeons are extremely small. They have no life-span as we envisage it, but they can exist for a long time in environments with suitable temperature, stability, and absence of damaging conditions.

The beginning of all this is a mystery. We don’t know how life forms came into being, or whether viruses came before or after organisms, or whether archaeons and bacteria had a common ancestor or arose separately. Some scientists think viruses came later than bacteria and archaeons, forming from remnants of the bodies of bacteria or archaeons.This may seem reasonable, because, nowadays, viruses require the presence of organisms for their existence, as I will describe later. Other scientists think viruses might predate living organisms because they are much simpler in many respects.

In this essay I will describe the four kinds of entities and their interactions.

Viruses

Viruses are very different from organisms. Viruses have none the necessary characteristics of  life, which are metabolism, reproduction, growth, and actions.

Metabolism is the process of taking matter and energy into the body, and using it for the purposes of growth, reproduction and providing power for functioning.

Reproduction is the process of producing new living entities within the body and releasing them as separate organisms.

Growth is becoming larger after becoming alive.

Viruses do not take in matter or energy, or reproduce, grow, or make any actions. They cannot move, they get moved around indiscriminately by the forces in their environment.

They are inanimate, even though they affect all kinds of organisms.

(Some people would want to include consciousness as a necessary aspect of life. Virtually everyone knows that they themselves are conscious, and believe that other people are conscious for at least some of the time, and assume that other species of animals have consciousness. But for many animals and other forms of life, there is no way of determining whether they have consciousness.

Consciousness has two essential components, the ability to be conscious and the ability to  have something to be conscious of. We, and most animals that we are familiar with, can detect aspects of the environment, and react accordingly. But, and especially with those that cannot speak to us, we have to understand and assume that what they and their actions indicate and tell us is true.

But we can never prove it. So I do not think that consciousness should be regarded to be an essential criterion for life.)

Only a small proportion of viruses have been studied, so there are probably many things they cannot move, but about them that we know nothing about. As at 2018, their classification system contained about 900 genera and 9000 species. The known species often have several strains, many with significantly different capabilities, and more strains are continually being created.

Viruses are extremely small structures, ranging from about 20 to 300 nanometres in size. To give some idea of these sizes, SARS-CoV-2, which causes Covid-19 disease, has a diameter of about one ten-thousandth of a millimetre.

A virus consists of a shell composed of protein, and it contains genetic material, that is, DNA and/or RNA. This genetic material provides instructions for replicating the virus. The SARS-CoV-2 virus genome is made up of almost 30,000 nucleotides — molecules that contain instructions for the amino acids that make up its proteins.

Some viruses, including coronaviruses, are covered by a phospholipid membrane (see later) in addition to the shell. These viruses are less stable and more vulnerable than other viruses.

Viruses can’t generate their own energy. They can’t move, but they get moved around indiscriminately by the various forces surrounding them.

Most viruses are inside the bodies of bacteria, archaeons, or eukaryotes, and some are in the bodies of other viruses. These refuges are known as hosts.

Most known viruses are useful or necessary to some kind of life. A small proportion are parasites. These infect bacteria, archaeons, and eukaryotes, and are damaging or lethal to their hosts.

The “good” viruses perform a wide range of functions for a wide range of organisms. A tiny proportion of them are used in medicine such as in attacking cancer cells and infectious bacteria. Many cooperate with other organisms, sometimes in symbiosis, sometimes acting as predators to keep the balance of ecosystems. (Symbiosis means two different entities helping each other.) They also act in conjunction with the immune systems of their hosts.

Viruses do not reproduce. They are replicated inside the cells of their hosts. All other cells are many times larger than viruses.

Cells have processes for using DNA and RNA to assemble new cells and other tissues, and also new viruses. This is a bit like 3D printing.

To get into a cell, a protein on the coating of the virus must match with a protein on the coating of the cell and make contact. For example, the coating of SARS-CoV-2 has a range of rough spikes. When one particular kind of its spikes comes in contact with a particular protein called ACE2, which is part of the coating of the host’s cells, the interaction opens the cell’s coating. Some of the proteins of the shell of the virus can break down the cell’s coating and let the virus or its RNA in.

 No other combination with that virus and cell will open the cell. So most kinds of virus can infect only one kind of host. But a mutation that produces a new strain will sometimes allow a virus to infect another species with similar characteristics to that host, and/or affect, positively or negatively, the virus’s ability to infect or damage.

Multicellular organisms can host several kinds of virus.

As soon as the first virus is constructed in the host’s cell, the construction of another cell begins, and this continues until it is interrupted.

During replication, the process sometimes accidentally produces a mutation in the new virus. Mutation may have no significant consequence, or it may produce an ineffective virus or a new strain of the virus. The high rate of replication quickly creates new viruses with new abilities.

The new viruses get out of the cell when the cell bursts or when they get pushed out through a breach in the cell wall. They then get moved around by the processes of the host’s body, and are likely to infect other cells. After a few days, there can be trillions of them.

This leads to the continual quick evolution of new strains and new species of viruses. As with  many organisms, viruses have evolved to ability to interact in large groups to both infect organisms, and to control their group activities, and to defend themselves against other viruses and organisms.

For example, replication is stopped when the population density of viruses reaches a certain level. Restricting the numbers of replications stops the host from being damaged or killed. This gives the virus a continuing habitat for survival, which reduces the probability of the virus dying out.

Viruses also can be in symbiosis with other viruses and with organisms. Symbiosis is different kinds of entities helping each other.

Some multicellular organisms can be hosting several kinds of virus. There is a large number of “good” viruses in the microbiomes of many kinds of organisms.

A virus may lie dormant in the host’s tissues for decades. Then some incident may cause it to resume replicating. This often produces lifelong or chronic infections in hosts. Common human examples are herpes and hepatitis B and C.

The genome of a retrovirus, whose genome is just RNA, sometimes gets put into its host’s DNA. This is usually advantageous for the host, such as increasing the host’s immunity. But it could be bad for the host when genomes of infective viruses such as HIV, are in the host’s genome and later get out and create more viruses. The genomes of most organisms, including ours, contains virus DNA.

Viruses are sent out of animal host’s bodies by the host coughing, spitting, and exhaling, in which case they are in tiny droplets of bodily fluid, mainly water. Then the air or the water or whatever they land upon decides where they go to. Where the humidity is low, some of the droplet liquid may evaporate more quickly, and allow the virus to float in the air for a longer. Viruses also get out in the host’s faeces.

Viruses get into the host by being inhaled, or put in the host’s mouth, eyes or nose after having been picked up from some object that they have landed on, and transferred to the fingers, (or other body parts for other species). People touch parts of their face many times a day. Thorough hand-washing with soap or detergent, etc., will remove viruses from hands. Viruses can also get in by being injected into body tissues along with infected blood or other medium.

People and other animals can be given some immunity from a specific kind of virus by being   vaccinated against that virus. Vaccination is a process of injecting some part of the specific virus into the body of the person or animal. This alerts the body’s immune system to some of the characteristics of that virus. A few weeks after a vaccination, the immune system will be able to recognise and attack that virus that virus if it gets in. But even then, the immune system must be able to come in contact with the virus. The effectiveness of this process depends on many factors, the kind of virus and host, the kind of vaccine, the health of the host and chance. Chance includes where the viruses are taken within the host’s body.

Vaccinating an infected host may sometimes reduce the severity of the effects of the infection. The immune system will already know about it and be taking action, which may not be successful. Sometimes the vaccine will help the patient’s immune system. After infection, antiviral drugs may prevent the replication of RNA viruses, but different groups of these viruses need their specific drug. But each case depends on many factors, the particular strain of the virus, the parts of the body that the virus is in, and the health of the host and its immune system.

The new viruses are sent out of the cell when the cell bursts or when they get pushed out through a breach in the cell wall. They then get moved around by the processes of the host’s body, and are likely to infect other cells. After a few days, there can be trillions, and there will be many mutations in the process.

This leads to the continual quick evolution of new strains and new species of viruses. As with  many organisms, viruses have evolved to work together in large groups to both infect organisms, and to control their group activities, and to defend themselves against other viruses and organisms, and to work in symbiosis with other viruses and with organisms.

For example, replication is stopped when the population density of viruses reaches a certain level. Restricting the numbers of replications stops the host from being damaged or killed. This gives the virus a continuing habitat for survival, which reduces the probability of the virus dying out.

Some multicellular organisms can be hosting several kinds of virus. There is a large number of “good” viruses in the microbiomes of many kinds of organisms.

A virus may lie dormant in the host’s tissues for decades. Then some incident may cause it to resume replicating. This often produces lifelong or chronic infections in hosts. Common human examples are herpes and hepatitis B and C.

The genome of a retrovirus, whose genome is just RNA, sometimes gets put into its host’s DNA. This is usually advantageous for the host, such as increasing the host’s immunity. But it could be bad for the host when genomes of infective viruses such as HIV, are in the host’s genome and later get out and create more viruses. The genomes of most organisms, including ours, contains virus DNA.

Viruses get out of animal host’s bodies by the host by coughing, spitting, and exhaling, in which case they are in tiny droplets of bodily fluid, mainly water. Then the air or the water or whatever they land upon decides where they go to. Where the humidity is low, some of the droplet liquid may evaporate more quickly, and allow the virus to float in the air for a longer. Viruses also get out in the host’s faeces.

Viruses get into the host by being inhaled, or put in the host’s mouth, eyes or nose after having been picked up from some object that they have landed on, and transferred to the fingers, (or other body parts for other species). People touch parts of their face many times a day. Thorough hand-washing with soap or detergent, etc., will remove viruses from hands. Viruses can also get in by being injected into body tissues along with infected blood or other medium.

People and other animals can be given some immunity from a specific kind of virus by being   vaccinated against that virus. Vaccination is a process of injecting some part of the specific virus into the body of the person or animal. This alerts the body’s immune system to some of the characteristics of that virus. A few weeks after a vaccination, the immune system will be able to recognise and attack that virus  if it were to get in. But even then, the immune system must be able to come in contact with the virus. What happens depends on the strain of the virus, the parts of the host’s body that the virus gets to, and the health of the host and its immune system.

Vaccinating an infected host may sometimes reduce the severity of the effects of the infection. The immune system will already know about it and be taking action, which may not be successful. Sometimes the vaccine will help the patient’s immune system. After infection, antiviral drugs may prevent the replication of RNA viruses, but different groups of these viruses need their specific drug. Viruses that are outside can be made ineffective by high temperature, strong ultraviolet light, diluted ethanol, diluted bleach, and some detergents. But some viruses have evolved to tolerate bleach and detergents. The treatment needs to damage the coating of the virus and/or disrupt the virus’s genome.

Viruses that are not inside a host will last longer in wet environments. The water provides a protective barrier from nearby solid mater, which otherwise could damage them if it is pushed against them. They also last longer on smooth surfaces than on rough.

No known viruses that infect archaeons and bacteria also infect eukaryotes.

Most viruses that infect humans and plants are named according to the diseases they cause or sometimes according to their structure, e.g., the varieties of corona viruses.

Most viruses that affect other species are named according to their genomes. Bacteriophage is one exception.

There is another group of viruses that are seldom written about. They are giant viruses that are about 100 times the size of the viruses that I have just described. They all seem to be oval in shape. There appears to be a wide range of giant viruses.

Other kinds of viruses have about 10 genes, but the giant viruses can have up to 2500 genes, most of which are different from the genes of other viruses and of organisms.

None of the giant viruses appear to infect other organisms except for amoebas and oceanic plankton, all of which are microscopic eukaryotes. (I will describe amoebas later.) As with other viruses, giant viruses are replicated by the processes of the cells that host them.

Bacteria

Bacteria are single-cell organisms with no nucleus. Their genome and organs are all in a gelatinous liquid covered by a membrane that consists of phospholipids. These are strands of a kind of sugar, with one end having a phosphate head that associates chemically with water, and the other having a fatty tail that tends to avoid water. To make a membrane, the strands line up, side by side with the heads and tails attracting each other. Outside the membrane, there are one or more coatings that provide protection but still enable various substances to get in and out. These comprise the cell wall.

This type of structure is used in all kinds of organisms, but the chemistry of archaeon membranes and walls is slightly different from that of the cells of all other organisms.

Bacteria come in a wide variety of shapes and sizes, but most are approximately spherical, rod-shaped or helical.

Bacteria average about three micrometres in size, which is about 100 times the average size of viruses. The range of sizes and shapes, and the numbers in each category, makes it hard to know how accurate this average would be.

Most bacteria are benign or helpful to other organisms, but some infect other organisms or are parasitic. As with viruses, we generally regard them all to be the enemy and to be eliminated, but most of them are essential, or helpful to eukaryotes.

Unlike viruses, which have no active ability, bacteria perform actions that require energy. So they take in food and energy to reproduce, move, feed, grow, and keep safe.

Bacteria detect environmental conditions and act accordingly. Different species have different needs, different environments, and different methods of moving.

In liquids they swim using a rotating tail, called an archaellum, which is made of protein. Other species have bristles, called pilli, on their surface that allow them to slide or shuffle along. Or the pilli may hook onto something and pull towards it by retracting into the bacterium.

Some bacteria are unable to move by themselves, and get moved around by water.

Most move around in a wide range of places, including inside other organisms, looking for food.

Bacteria have pores in their outside wall for taking material in and ejecting it. Overall, they eat a vast range of organic material, each kind of bacterium having its particular kind in accordance with its species and its habitat.

Bacteria affect organisms and viruses by what they eat and what they excrete. What they eat may be indigestible to other organisms. Also, their eating can degrade food or damage the bodies of their hosts.

What they excrete may contain toxins, or it may contain nutrients that other organisms can’t otherwise obtain. It may also be used in defence.

All of this can occur in the soil, in water, or inside their hosts, as with the gut microbiomes of animals.

All organisms employ electrons in all of their processes. Usually they obtain them from chemical reactions with their food. Some bacteria that live in water have processes for directly accepting electrons. In their environment, if an object with a negative electric charge enters the water, any nearby bacteria will extend strands of conductive tissue to meet the object. They will then extend more strands to other bacteria, feeding them with electrons. Some bacteria get all of their energy this way.

Reproduction of bacteria can occur by splitting, or by forming buds that protrude from their surface. The buds grow until they are ready to break free.

Some bacteria pick up and incorporate strands of DNA from the environment, such as from a virus attached to DNA, or  from another bacterium,  or picking up DNA that is lying or floating around. This gives plenty of opportunities for mutations.

Bacteria reproduce at different rates, depending on the species and the food supply and the temperature. It can occasionally be as fast as ten minutes per generation. Under some adverse conditions, some bacteria may change into something like spores to reproduce.

Most kinds of bacteria use products of their metabolism, that is, their shit, to disable infecting viruses, fungi, and other bacteria. Some bacteria use specialised proteins. The outcome depends on whether the defending bacteria have enough ammunition, and that will depend on how many invaders there are. Other kinds of bacteria use bits of virus DNA against viruses. And there are many other kinds of defensive tricks.

Bacteria communicate with each other. One method of communicating is by secreting and sensing various kinds of chemicals. They also use electrons and light. They coordinate their actions, such as in defence and in building biofilms.

Biofilms are like tiny fortresses, providing security to the bacteria. They are flat circular mats, consisting of bacteria and their by-products. They are covered with sticky organic material, which protects from above and glues them to whatever they are attached to.

The members have special roles, depending on where they are within the circle, and this adapts the different members accordingly. Some find, or produce, food. Others protect the surface and the edges of the biofilm.

Biofilms grow by attracting bacteria from outside. There can be billions of bacteria in a single biofilm. More than 99% of bacteria live in some kind of community.

Different species and strains of bacteria build biofilms with different structures and managements. The kind of biofilm also depends on the environment, e.g., on a tooth or in running water or inside the body of the host. Unseen biofilms are almost everywhere.

While there is a large amount of coordination and cooperation within these communities, there is also competition between the members. There is intense competition between communities, including different kinds of bacteria and other microorganisms. Nevertheless, biofilms will associate with neighbouring biofilms and other communities for greater protection.

All of these kinds of action seem remarkable for such tiny organisms. But everything is controlled, by population, population density, food supply, environmental conditions, and the genomes and structure of the organisms.

Bacteria inside a host’s body can be killed by antibiotics, which damage the structure of the bacterial coating or the bacterial internal organs. This can stop the function of the bacterium, including its ability to reproduce. (Antibiotics have no impact on viruses.)

Bacteria can also be killed by viruses, as already mentioned, and by the immune system.

Outside the body, bacteria can be killed by high temperatures, alcohol such as methylated spirit, acetic acid such as vinegar, and a few other liquids. Some bacteria can tolerate some of these.

The same applies to archaeons, but, because archaeons do not threaten us, we haven’t studied them as intensively as with bacteria.

ARCHAEONS

Archaeons are single-cell organisms,very similar in their size, structure, genome, and organs to those of bacteria. But some of the chemistry of the coating, and of the RNA, of archaeons, is different from that of bacteria and of eukaryotes.

Archaeons are probably the most abundant life forms on Earth. Trillions of them are everywhere, in the atmosphere, in all waterways and in the soil.

Archaeons live in almost every location that supports life, including extreme environments, such as hot springs and very salty lakes where no other kinds of organisms can live. They are in the bodies of all eukaryotes, but no known archaeons are pathogens or parasites.

We have archaeons in many of our internal organs, and on our skin. They are essential for most of the eukaryotes on Earth. As a part of the microbiome (see later) of all eukaryotes, they help to perform basic bodily functions, such as digestion of food.

Trillions of them are everywhere, in the atmosphere, in all waterways and in the soil.

As with bacteria, archaeons take in food and energy to reproduce, move, feed, grow, and keep safe.

They eat a very wide range of food. This includes virtually all organic substances, some derivatives of iron, and sulfur, uranium, carbon dioxide, methane, hydrogen, ammonia, and many other compounds. Their eating and excreting help to sustain the conditions of the environment, including reducing the amount carbon dioxide in the oceans, atmosphere, and soil.

Their reproduction methods differ with different species, but, in general, are similar to those of bacteria.

Apart from not being parasitic or infectious or spoiling food, archaeons have all the same properties and functions of bacteria.

It is usually thought that eukaryotes arose through the amalgamation of an archaeon and a bacterium. Some of the DNA of archaeons is so similar to that of eukaryotes that is now being suggested that eukaryotes are really versions of archaeons. But there are very great differences as well as similarities.

Archaeon genes and metabolisms are more closely related to those of eukaryotes than those of bacteria. But some parts of their biochemistry don’t appear in viruses, bacteria, or Reproduction methods differ with different species. The most common method is binary fission. In this process the archaeon develops a second genome and other components, and then splits. Other methods involve taking in and using DNA from the environment or from other archaeons to build new archaeons.

Archaeons are our unseen, little-known, but essential, friends.

Ongoing research has recently found that there are more than twice the number of archaeons and bacteria living deep under the earth’s surface than there are on and above it. And there are at least as many kinds of these organisms down deep as those above. Some of them are fairly closely related to surface archaeons and bacteria. Viruses and fungi also have been discovered there.

The volume of territory that they occupy is thought to be about twice the volume of Earth’s oceans, which occupy 70% of the earth’s surface and  on average are about 4 km deep.

Their underground conditions are very different from those above, with higher temperatures and very high pressure and difficulty of moving around. So these organisms meet much fewer other organisms than those above do. There are fewer dangers, the main one being depletion of their food supply. Everything happens very slowly, so they live a lot longer and reproduce at a very much slower rate.

Even more surprisingly, geomicrobiologists have recently revived bacteria that had been lying dormant for more than 100 million years in clay about 74.5 metres under the seafloor in the South Pacific Ocean, which at that point is under 5.7 km of water.

They may be the oldest known organisms on Earth.

The scientists incubated them for up to 557 days in a laboratory until they were acclimatised to life on the surface.

The bacteria are aerobic, i.e., they need oxygen to live. Oxygen was present in the sediment  in which they were found. They must have had no nutrients during most of the 100 million years, but they were still alive.

They are of varied lineage, spanning 10 major groups of bacteria, and have a diverse range of food and of processing it.

This discovery is from a minute proportion of the sea floor, which has a huge range of depths, which have been subject for billions of years to the ups and downs of plate tectonics (which is sometimes referred to as continental drift). We can only wonder how much else is under the ocean floor, and what is it like.

Eukaryotes

Eukaryotes are much larger than, and have great differences from, viruses, archaeons, and bacteria.

All of Earth’s multicellular organisms are eukaryotes. There are, however, many kinds of single-cell eukaryotes. With the exception of these, the cells of all eukaryotes have features that enable them to join with and work with other cells to build an almost unlimited range of complex shapes, sizes, and types. This gives eukaryotes a huge range of differences and abilities.

To the best of our knowledge, the first eukaryote came into being about 2.7 billion years ago when a bacterium and an archaeon fused into a single organism, with one of them becoming the nucleus of the new organism. The descendants of that organism evolved in different ways to gradually produce groups of organisms more different from each other in appearance and function, and structure, than the differences between and within archaeons and bacteria. And yet the basic apparatus within all eukaryote cells is virtually the same. Almost all of the differences between the individuals and between the groups are the result of different details in the DNA in the nuclei of the cells.

Eukaryotes are the only organisms whose cells have an enclosed nucleus encasing their DNA. The nucleus has a lot of similarities with the bodies of archaeons and bacteria. It is contained in a phospholipid membrane, and has outer coatings with pores through which material gets in and out. Its DNA is more similar to that of archaeons than of bacteria.

The nucleus contains a gelatinous liquid similar to that of archaeons and bacteria.

The nucleus also has differences from archaeons and bacteria. The DNA or RNA of an archaeon or a bacterium is just one chromosome and is circular. The DNA of eukaryotes is in long twisted strings, and has several chromosomes.

And the nucleus has no flagella or pilli, or any other means of propulsion. It doesn’t go anywhere.

In addition to the nucleus, the cells contain tiny organs called organelles, that perform a range of functions.

The Golgi apparatus prepares proteins for secretion out of the cell, and helps in the distribution of lipids around the cell, and creates lysosomes.

Lysosomes break down excess or worn-out parts of the cell and any infesting viruses and bacteria.

Mitochondria produce and store energy for the functioning of the cell. They use a chemical process involved with the metabolism of the cell. They have their own DNA, which is different from the other DNA in the nucleus.

And there are a lot more components that are part of the operations within the cell.

The cell also has an internal supporting structure made of microtubes that gives it its shape.

All of this is washed in a gelatinous liquid.

All eukaryote cells are many times the size of prokaryotes.

Eukaryote cells reproduce by cell division. To do this, the cells need to take in nutrients and other substances, creating a new nucleus and organelles, etc., inside the cell, using the 3D processes. This is a process controlled by the cell’s DNA, using RNA to produce amino acids and create and assemble proteins.

In multicellular eukaryotes, the organism and its components grow by reproduction of the cells. Although all the cells have the same genome, different types of cells are produced to build the different parts of the organism. This is controlled by different cells having different genes being activated or silenced.

Multicellular eukaryotes need distribution systems to transfer information and nutrients and other material throughout their bodies.

The eukaryotes have been classified into four distinct Kingdoms: Animalia, Plantae, Fungi and Protista. The first three are each thought to have their own common ancestor, and the members of these three have features that distinguish their members from the members of other kingdoms. The protists have miscellaneous ancestries, and none of them could be regarded to belong to any of the other kingdoms.

Animalia

Animals come in a huge range of sizes, from microscopic rotifers, whose bodies have only about 100 cells, to the largest whales.

They are built of soft flexible tissue that consists mainly of water. Their bodies are mostly supported by stiff material, either inside or coating the body. Almost all of them can move parts of their body. They can perform a range of functions, and most of them can move around their environment. Many kinds of animals can fly, walk, run and/or swim. Animals that live fixed to one spot, such as sponges and oysters, move parts of their bodies to obtain food and for defence.

Animals depend on getting food from their environment. Their food comes from parts of the bodies of a wide range of eukaryotes. Some are predators, some are parasites, and some are scavengers. Their mouths take in food, and then an internal system digests the food, which produces nutrients and building material, which are distributed around the body. The depleted residue is ejected.

Animals have mouths that take in food and a hollow internal systems where food is digested and from which nutrients are distributed around the body, and the depleted residue is ejected. Their food comes from parts of the bodies of a wide range of eukaryotes.

With the exception of loricifera, a small group of microscopic inhabitants at the bottom of deep seas, all animals must continually take in oxygen, which is then distributed throughout their bodies as an essential source of energy. Carbon dioxide is produced in the body’s processes and then emitted.

All kinds of eukaryotes are inhabited by viruses, archaeons, and fungi. Some may benefit from this and others suffer. In animals, the benefit ranges from being trivial to being essential or lethal. Many eukaryotes have a microbiome, that is, a collection of trillions of viruses, archaeons, bacteria and fungi working together in their digestive systems. Microbiomes are vital for the physical, and where appropriate, the mental, processes of the host.

Animals have systems of nerves that send signals throughout the body, controlling the movements of various body parts, and sensing their exterior and interior environments.  In all but the smaller animals, this is controlled by a brain, which consists mainly of nerves, and, in some mammals, of billions of nerves.

Animals have a wide range of senses and combinations of senses. Some of the main senses are sight, hearing, touch, taste, smell, and balance, and there are several more. Some animals can detect magnetic forces.

Animals are the only organisms known to purposely create sound, which they use for communication with each other. The very small animals might not have this facility.

The most intelligent organisms are animals, particularly vertebrates, and the most intelligent animals are the species Homo sapiens, that is, humans. But many kinds of animals have skills, abilities, and kinds of intelligence that most humans lack.

Most animals reproduce sexually, that is, with the fusion of a male cell and a female cell, which becomes an egg. An egg is a single cell that develops into a new-born animal that grows to be an adult. Depending on the species, the egg may develop inside the body of the female animal to a stage where it can survive outside. Or the egg may be put outside of the parent’s body, and develop inside the egg’s coating.

Some small invertebrate animals have multi-stage reproductive processes, starting with an egg that is put outside the animal’s body. In one kind of sequence, after a time the egg produces a larva, such as a caterpillar or grub, which eats and grows ,and then builds a cocoon into which it enters and becomes a chrysalis. The chrysalis begins as a liquid and slowly develops into an adult animal that then breaks out of its container.

Some animals, such as snails and worms, are hermaphrodites, that is, they have both male and female sexual organs.

Most larger  kinds of animals have life cycles.  These have sexual reproduction.

This includes not only the processes of fertilisation, initial development, becoming separate from the parent and then growing to an adult stage. They also have a decline as their tissues and internal systems decline until the body can no longer function.

Some animal microorganisms reproduce asexually. This occurs in various ways. Some reproduce by fission, that is, producing a replica of themselves inside their body and then splitting into two organisms, similar to some prokaryotes. Others, such as  planaria and hydra, reproduce by shedding fragments of their bodies. Some larger animals, such as jelly fish, can also reproduce from fragments. Chopping them up in an attempt to destroy them produces multiple new jellyfish. These animals have no life span. Like prokaryotes, they live until they are killed by the actions of their environment.

But most of the larger animals are not able to grow a replacement when a body part is lost. The exceptions are some lizards that can replace the ends of their tails.

Plantae

Most plants are rooted in the ground. They do not move around and the movements they make of their body parts are, with a few exceptions, opening and closing the petals of their flowers and turning the stems and flowers towards the sun. Many kinds of plants will grow towards sunlight and/or to occupy empty spaces.

Plants make their own food and internal material, using a process of photosynthesis of  atmospheric carbon dioxide, water and nutrients from their environment. Oxygen is emitted from this process. The process is powered by sunlight that falls on the plants’ leaves. Most of Earth’s oxygen is provided by plants. The rest comes from microorganisms.

With plants taking in carbon dioxide and emitting oxygen, and animals taking in oxygen and emitting carbon dioxide, it looks a bit like symbiosis. But most animal food is derived, directly or indirectly from eating plants, so the symbiosis is a bit one-sided.

Most plants have stems and branches with green leaves attached in specific patterns. The stems and branches may be stiff or flexible, and tough or fragile. Plants have a range of outer coatings , from being very smooth to very rough. The stems and branches of trees are mostly composed of wood, which is the coating of the plants’ cells and is composed of cellulose and lignin. Plants also contain water.

Some of the plant’s cells have an organelle called a chloroplast, that puts a green substance into the leaves and other body parts to increase their absorption of sunlight. One species of snail, which is an animal, has a chloroplast in its genome. It is normally green but goes red in Autumn.

Most plants obtain nutriments, mainly nitrogen and minerals, through their roots in the ground. The roots need water to enable them to take in the nutriment. The roots, which stabilise most plants in the ground, are also the plants’ control organs. The roots send water and nutrients up to the rest of the plant and into the leaves. Most plants require a continual supply around their roots. But there some that can get enough water from the atmosphere.

Other plants, such as mistletoe, get their supply of water and nutrients by tapping into the part under the victim’s bark where the tree’s nutrients are distributed.

Plants have rudimentary nervous systems. They also have rudimentary memories of events that affected them. Some plants whose leaves are being eaten by insects will send toxins into their leaves. Others emit chemical signals to warn neighing plants to release toxins. (Some species of animals, funguses and protists also have toxins in their tissues to repel predators)

Most plants reproduce sexually, often with the incidental help of animals, mainly insects, that come to their flowers to feed on or gather the nectar and pollen produced by the flowers. This happens to bring male and female reproductive cells together to form seeds. The seeds ripen, and become detached, and get distributed to the surrounding area, where some of them will take root and grow into new plants.

Some plants are self-fertilising, that is, they can have both male and female flowers.  Pollen from the male flowers  gets into the female flowers, fertilising them.

Most plants can grow new parts after parts have been removed.

Some plants have life spans. These are usually small soft-bodied plants that die off after they have flowered, produced seeds, and sent the seeds out into the environment. Others continue in accordance with the availability of water and nutrients.  Others are trees, some lasting for centuries until their internal systems die down.

And there are other plants that produce branches that take root and begin to grow independently. These have no particular life span as such, and depend on the condition of their environment.

Many plants can grow from stems or leaves that are purposely planted in the ground. For some plants, this is the only method of reproduction.

Plants have microbiomes in parts of their bodies above ground and in the soil around their roots. This is different from the symbiosus between a multicellular fungus and a plant.

No plants are microorganisms.

Fungi

Funguses, like the other kingdoms, are multitudinous and everywhere.

The larger ones consist of fleshy flexible filaments tangled together. They grow by extending one end of each filament and by building new filaments.

Funguses range in size from single cells, which are called yeasts, to great accumulations of filaments. The largest organism on Earth is thought to be a fungus in Oregon USA. It occupies an area greater than 400 hectares under the ground. It is thought to be about 2,400 years old.

Funguses not need sunlight. Most of the mass of the earth’s fungus is underground. But some species live in the tissue of other organisms, including in rivers, lakes, and oceans, but not entirely under water.

Funguses need to take in water and prefer moist and slightly acidic environments. But they do not live under water.

Like plants, funguses cannot move around. And they cannot act to move their body parts, not even like the slight movements of plants.

Like animals, funguses require oxygen and excrete carbon dioxide.

Unlike plants, but like animals, they cannot make their own food. They get their food and energy from taking in material from living and dead organisms, and from decayed organic matter. These characteristics, and the softness of their bodies, is said to make fungi more similar to animals than to plants.

Many species of fungus live in a symbiotic relationship with plants. About 90% of plants depend on fungi for some of their nutrients, and the fungi receive nutrients from the plants. Lichens are symbiotic combinations of fungi and algae.

Many kinds of single-cell fungi infect eukaryotes, but many more are in or on the bodies of eukaryotes as part of the usually helpful microbiota.

Funguses multiply sexually and/or asexually, mostly by producing spores, which get distributed into the environment. Spores are encapsulated cells that can become new organisms, somewhat similarly to seeds. Sexual reproduction involves the union of two spores. Mushrooms and toadstools are spore-bearing fruiting bodies of fungi. As with plants, the sexual process does not involve deliberate action.

Mushrooms and toadstools are  spore-bearing fruiting bodies of funguses.

Funguses can repair damaged parts of their filaments, but not damaged mushrooms.

They have no life span, and keep on growing and existing for as long as their environments allow.

Funguses have no microbiomes.

Almost every species of organism on Earth, except funguses, can be infected by some kind of fungus.

Protista

Protists are miscellaneous eukaryotes that do not belong to any other kingdom. As with other eukaryotes, they are very diverse.

Most protists are single cells, but a few can be larger. One exception is the giant kelp that can grow to about 50 metres in length. Kelp is one kind of alga, all of which contain chloroplasts similar to those in plants and cyanobacteria.

Algae reproduce in a wide range of ways, from cell division to sex. Most of the other protists use cell division.

Most protists live in water or damp soil. To move through water, most of the smaller ones use similar methods to archaeons and bacteria.

Some protists produce their own food within their own bodies, others have to find it.

Many protists are parasites. One genus, Plasmodia, contains species that infect animals and cause malaria in humans. Many protists are symbiotic. One odd example of symbiosis is that sea otters shelter from predators in the huge thick layers of kelp. The otters eat sea urchins, which feed on kelp.

One group of protists is the slime moulds. There are about 900 species with similar characteristics but with a range of ancestries.

They can reproduce sexually, and end their lives as clusters of spores, which are released into the wind or the water. When two matching spores come together, they become like a new juvenile cell, which feeds and grows into being a single-cell adult.

Most microscopic protists reproduce asexually, either by binary fission, or by growing buds that break off, or by broken off parts of their bodies.

Single-cell slime moulds can live individually, feeding on bacteria on dead vegetable matter. When food is scarce, some species unite to be something like larger multicellular organisms. These “quasi-organisms” have a range and sizes, the largest being a few centimetres. They can move, usually in a way resembling that of a slug or snail. They can detect the presence of food in their environment and move towards it. Some cells then form into fruiting bodies that release spores, a bit like tiny mushrooms.

Amoebas are protists that can change shape to produce the equivalents of legs. Their enclosing membrane is covered with hairs, which are used in conjunction with shape-changing, to assist in moving around, feeding, and in other functions. They are mostly unicellular. A large proportion of them infect other organisms.

Despite their similarity, different groups of amoebas have different ancestries.

Epitaph

With the possible exception of protists, my descriptions and classifications may make all this look like a tidy consistent system. But at every stage there are ambiguities and exceptions.

There are many different definitions of the concept of species. These refer to genomes, methods and possibilities of reproduction, ancestry, and kinds of body structure, which are invoked to suit the different kinds of organisms.

Because they are inanimate, there may be questions about whether the viruses, should be regarded as inhabitants. If the answer is yes, there are other inanimate things that might also be justified as inhabitants. These are various kinds of strings of DNA and/or RNA, such as CRISPRs and Borgs, and bits of proteins, that also are floating around, and may affect organisms, mostly microorganisms. As with viruses, they can land right inside microorganisms, and even into the genomes of microorganisms, which may affect the hosts’ processes. Some of them code for proteins. Some microorganisms use them in their interactions with other microorganisms.

Scientists use specific CRISPRs and viruses as tools in gene editing, that is, in making changes to the genomes of organisms.

Very many organisms, large and small, have, in their genomes, DNA and other fragments that came from their environments. This has influenced the organisms’ characteristics and fates. There is the continual exchange of DNA within and between archaeons and bacteria, and characteristics of one kingdom of eukaryotes getting into another, such as the snails that have chloroplasts and are green in summer and go red in autumn, like the autumn leaves of plants.

Almost all of the plants synthesise their own food, but there are several plants, with a range of ancestries, that are carnivorous. Most of them have features that attract and trap small animals. They use varieties of enzymes to break down the bodies of their victims to produce the nutrients that they rely on.

There are continual dynamic changes of evolution and extinction. There are continual changes in the environment throughout and beyond the earth. We are part of both the biological and the physical systems, as subjects and as actors.

The characteristics of all of Earth’s inhabitants have been determined by the conditions on Earth, and on its history, in accordance with the laws of physics. Their emergence and development seem to have happened through a succession of very unlikely coincidences. But all of the coincidences were statistically possible.

The four kingdoms of eukaryotes and the prokaryotes and the viruses have continually interacted to produce ecosystems. These ecosystems have had to adapt to the changing conditions of the planet and have from time to time been disrupted or destroyed. The most recent disruption is being caused by the activities on one species of the eukaryotes, Homo sapiens.

Looking at these distinctive groups, one might wonder what the world would be like if one of them did not exist, for example, one of the first three eukaryote kingdoms, or if there was only one kind of prokaryote. We might also wonder what the world would be like if one of the large global extinctions had not happened.

When we conjecture about extraterrestrial life, we expect it to have a lot of similarities with our forms of life. But the physical properties and the history of each extraterrestrial body will have substantial differences from those of Earth.

Any inhabitants of other parts of the universe would have similarly arisen and developed in accordance with the possibilities allowed by the conditions and histories of the object they occupied. I think it would be very unlikely that the first life on Earth arrived from somewhere else in the universe, and the same would apply to any extraterrestrial life.

We, Homo sapiens, are just one recently evolved species among the eukaryotes, peeping from our little planet into the outer universe.

We know quite a lot about Earth’s inhabitants and their histories.

But we have scant knowledge of how it all began, or what inhabitants there are beyond our planet, or where we are going.

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