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Viruses are curious biological entities. They are obligate parasites; unable to replicate on their own, they instead exist by hijacking the cellular apparatus of other cells to replicate and proliferate. As such, they are simplistic - so simple, in fact, that they don't satisfy all the criteria to be considered 'alive'.
Viruses cannot synthesise adenosine triphosphate, a critical molecule used for carrying energy. They likewise do not possess the molecular equipment to perform translation, the process that uses information from the genetic code called ribonucleic acid (RNA) to synthesise proteins. Proteins are the workhorses of cellular life, and without them a cell is devoid of almost all activity.
This absence is analagous to possessing a recipe book but having no kitchen appliances with which to cook.
Lacking energy-carrying molecules and the ability to make proteins would be devastating to a self-sustaining organism, but viruses do not carry out any metabolic processes. Instead, when it's independent, a virus is just a small, lifeless husk of genetic material wrapped inside a meagre protein shell. If it were to somehow remain in isolation, it would soon dwindle to extinction.
Once a virus finds a host, however, it assumes a much more impactful role. They may not possess much complexity, but what viruses do have is the ability to infect cells and once inside take advantage of the cell's protein-building ability to replicate themselves. Unfortunately for the host cells, they are often the architects of their own destruction as their apparatus busily gets to work copying the virus' genetic material at the expense of itself. Some viruses are also able to integrate into their host cell's DNA, becoming an intrinsic part of it. These attributes make viruses the master manipulators of cellular life. This has allowed them to persist for many billions of generations despite being entirely dependent on other organisms for replication; some viruses are so devastatingly effective at proliferating through this method that they're even capable of eradicating immensely complex multicellular life.
How did viruses evolve to be this way? Were they once fully-equipped micro-organisms that shed their molecular 'dead weight' and became parasites, or did they begin as just genetic code and gain a few fancy tools that helped them ensure their own replication? Or did viruses first evolve before even single-celled organisms, and those that persist today and mere relics of an ancient emergence of life?
Genetic code is the basis for life on Earth. It is, as far as we understand, the first organic molecule capable of carrying swathes of chemical instructions and so underpins all life. Genetic code is made up of nucleic acids, DNA and RNA. In complex life, DNA is first transcribed into RNA, which then relays the chemical instructions to molecules called ribosomes that form proteins. In this setup, RNA is the intermediate component, but it's now believed that RNA was the first nucleic acid to exist at the origin of life. Scientists have also identified a group of RNA molecules known as ribozymes that can catalyse chemical reactions - a job principally performed by proteins. Therefore, at the origin of life, the very first entities may not have needed DNA or proteins at all in order to replicate.
If such self-replicating units existed prior to the evolution of the very first cells, they may have been primed to infect these cells once they appeared. Therefore, the parasitic role of the virus may have been established as soon as they first contacted cellular life. Some viruses still solely use RNA as their genetic code and may be the closest descendants to their ancient parasitic foreunners.
Viruses that exist today all gain by damaging their hosts, but it may not have always been this way. Many species in nature exist in symbiotic relationships, where both parties can benefit from the other's presence. An example of this would be the exchange of nutrients between fungi and plant roots in the soil, or African birds such as piapiacs that eat lice from the backs of large land mammals. Viruses may have one enjoyed such a mutually beneficial relationship with another organism. Over time, however, the viruses that decided to lose their own molecular machinery in favour of using their partner's could have gained an adaptive advantage; making molecular apparatus is costly for a cell; it requires lots of genetic instructions, lots of energy and lots of resources. The viruses that accidentally lost these once-essential pieces of kit may have found that they could persist much better by instead using another's tools.
Although all known viruses today are obligate parasites, some larger viruses offer support for the regression hypothesis by resembling self-sufficient ancestors. The Mimivirus, for example, is a behemoth among viruses. Relative to other viruses, it is gargantuan in both how much genetic code it carries and simply how large it is. Adeno-associated viruses can be absolutely miniscule, measuring just 20 nanometres in diameter -
That's 15,000-times smaller than a grain of salt!
They also have tiny lengths of genetic code containing just 4,500 nucleotide bases. In stark contrast, the giant Mimivirus can measure 500 nanometres and boasts a whopping genetic code of 1.2 million nucleotide bases. Not only does the size of the Mimivirus resemble fully living microbes, its DNA also contains instructions for an incomplete set of proteins responsible for metabolism and translation. Larger viruses also tend to depend on their hosts less than their smaller counterparts, with some being able to convert their DNA into RNA without direct input from the host. It has been proposed that these larger viruses, in particular the Mimivirus, could be examples of viruses that have retained many elements of what ancestors of all viruses once possessed.
Viruses straddle the boundary of what biologists consider to be life. On the one hand, they cannot regulate their internal state - a process known as homeostasis - or indeed carry out any metabolic processes, and independently they don't respond to stimuli. On the other hand, they do reproduce. This latter attribute is hugely important, because the ability to pass on genetic material is all that's needed for evolutionary processes to get to work. So the origin of viruses may not have arisen from an independent biological entity at all but from fragments of genetic code that became immensely effective at facilitating its own replication.
Transposable genetic elements are segments of genetic code that can move position within DNA. They are sometimes referred to as 'jumping genes' as they hop to either locations along the DNA strand or they jump to another strand of DNA entirely. The human genome is packed full of a form of jumping genes called retrotransposons. Retrotransposons can carry genetic instructions that allow them to be both copied and then pasted into the new DNA, enabling them to be snugly integrated into the genetic fabric of a new cell. A family of viruses called retroviruses operates in a similar way, such as the Human Immunodeficiency Viruses (HIV), which effectively infect and then integrate into their host's DNA. Proponents of the progression hypothesis recognise the familiarity between virus-like retrotransposons and retroviruses. What if a change even gifted a retrotransposon new genetic material that allowed it to encase itself in a protein shell and easily migrate to new cells? The genetic code would not be alive, but it would be able to flourish and perhaps evolve into the viruses that exist in the world today.
The regression hypothesis argues that viruses are simple entities because they lost most of the molecular machinery needed to maintain life. The progression hypothesis instead argues that the first viruses never had this machinery to begin with, but instead evolved from an assembled set of components needed for migrating and replicating genetic code. The precursor hypothesis, in contrast, suggests viruses lack complex cellular apparatus because they're remnants of an ancestral form of life that evolved before these units appeared.
Viruses are incredibly diverse entities. Some are tiny, others large; some possess DNA, and others RNA. Depending on what group of viruses we zoom in on, certain theories seem more plausible. The gargantuan Mimivirus and other larger viruses like the Poxvirus are indicative of the regression hypothesis, retroviruses such as HIV the progressive hypothesis, and other RNA viruses the precursor hypothesis. One or all of these hypothesis may be correct. It is possible that rather than originating from a universal ancestor, viruses evolved multiple times independently. If this is the case, their shared features may be the product of a phenomenon known as convergent evolution, where natural selection causes different organisms to acquire the same trait. An example of this would be wings. Birds and insects haven't shared a common ancestor for millions of years, yet both converged on the same trait of flight.
If viruses in fact have multiple origins, then they may have picked up similar features through their shared 'lifestyles' of being obligate intracellular parasites. Alternatively, as as-yet unconsidered hypothesis may hold the answer, and only by continuing the search to discover new viruses will we discover the true origin of these fascinating biological entities.