Are viruses "alive?" and other related questions

[LLJKSiLk]

To start off, I'm coming at this from the point of view of an Atheist who is the product of a substandard scientific education in the Bible Belt of the United States. Much of what I've learned scientifically has been through my own reading and learning and this is something I'm curious about hearing perspectives on.

As a given, what I've learned is that many (most?) scientists do not consider viruses as being alive because they do not have the capability to reproduce without the aid of a host cell and don't typically use the cell-division method of replication.

However, viruses must in my understanding have come about and survive/thrive based on the same principles of Darwinian evolution and natural selection. If they weren't viable they wouldn't continue, and I would assume that they evolve based on the changing environments they must survive/thrive in. Is this the case?

As they don't replicate in the same sense that normal cells would, how would the first instance of a virus come about?

Do viruses mutate rapidly? As in they must at some point cross a species barrier? By my understanding, not all viruses that affect one species would affect another.



These are a few questions to open the discussion. I'm thankful in advance for any replies or pointing me to sources of information to learn more.

 

[Mr_Wilford]

First off, welcome to the forum

You're correct that viruses survive and thrive via darwinian mechanism of evolution. This is because they contain genetic material that can mutate and change with popluations. However, there are several reasons scientists do not consider them to be living.

For one, viruses do not undergo homeostasis to control their internal environment. Nor do they have a metabolism, grow, excrete wastes, or perform many other functions that your typical cell will go under. As of now, these are the typical things something must do to be considered "life"

It's my personal opinion that viruses represent a grey area between life an non-life.

You're also correct that they evolve to their host environments as well. While I'm no expert, it's my understanding a big part of this is the fact that antibodies, the protiens your white blood cells release to attack a pathogen such as a virus, are specific to certain protein binding sites depending on the virus. However, if a virus mutates and these binding sites change, the antibodies no longer work and you've effectively got a new strain. So that's one way they evolve and adapt to their host environment.

Viruses such as cold (I've got one right now, it's miserable) and flu are prime examples of this. It's why we need a new flu vaccine every year: they keep mutating and the old anitbodies are ineffective.

Yes, they can cross the species barrier. Examples of this would be H1N1 influenza, Ebola, HIV, etc.

How would the first virus come about? I'll drop some wiki information and leave you a link to its page on virus evolution.

Viruses are found wherever there is life and have probably existed since living cells first evolved.[40] The origin of viruses is unclear because they do not form fossils, so molecular techniques have been used to compare the DNA or RNA of viruses and are a useful means of investigating how they arose.[41] In addition, viral genetic material may occasionally integrate into germline of the host organisms, by which they can be passed on vertically to offsprings of the host for many generations. This provides an invaluable source of information for paleovirologist to trace back ancient viruses that have existed up to millions of years ago. Currently, there are three main hypotheses that aim to explain the origins of viruses:[42][43]

Regressive hypothesis

Viruses may have once been small cells that parasitised larger cells. Over time, genes not required by their parasitism were lost. The bacteria rickettsia and chlamydia are living cells that, like viruses, can reproduce only inside host cells. They lend support to this hypothesis, as their dependence on parasitism is likely to have caused the loss of genes that enabled them to survive outside a cell. This is also called the degeneracy hypothesis,[44][45] or reduction hypothesis.[46]

Cellular origin hypothesis

Some viruses may have evolved from bits of DNA or RNA that "escaped" from the genes of a larger organism. The escaped DNA could have come from plasmids (pieces of naked DNA that can move between cells) or transposons (molecules of DNA that replicate and move around to different positions within the genes of the cell).[47] Once called "jumping genes", transposons are examples of mobile genetic elements and could be the origin of some viruses. They were discovered in maize by Barbara McClintock in 1950.[48] This is sometimes called the vagrancy hypothesis,[44][49] or the escape hypothesis.[46]

Coevolution hypothesis

This is also called the virus-first hypothesis[46] and proposes that viruses may have evolved from complex molecules of protein and nucleic acid at the same time as cells first appeared on Earth and would have been dependent on cellular life for billions of years. Viroids are molecules of RNA that are not classified as viruses because they lack a protein coat. However, they have characteristics that are common to several viruses and are often called subviral agents.[50] Viroids are important pathogens of plants.[51] They do not code for proteins but interact with the host cell and use the host machinery for their replication.[52] The hepatitis delta virus of humans has an RNA genome similar to viroids but has a protein coat derived from hepatitis B virus and cannot produce one of its own. It is, therefore, a defective virus. Although hepatitis delta virus genome may replicate independently once inside a host cell, it requires the help of hepatitis B virus to provide a protein coat so that it can be transmitted to new cells.[53] In similar manner, the sputnik virophage is dependent on mimivirus, which infects the protozoan Acanthamoeba castellanii.[54] These viruses, which are dependent on the presence of other virus species in the host cell, are called satellites and may represent evolutionary intermediates of viroids and viruses.[55][56]
In the past, there were problems with all of these hypotheses: the regressive hypothesis did not explain why even the smallest of cellular parasites do not resemble viruses in any way. The escape hypothesis did not explain the complex capsids and other structures on virus particles. The virus-first hypothesis contravened the definition of viruses in that they require host cells.[46] Viruses are now recognised as ancient and as having origins that pre-date the divergence of life into the three domains.[57] This discovery has led modern virologists to reconsider and re-evaluate these three classical hypotheses.[57]

The evidence for an ancestral world of RNA cells[58] and computer analysis of viral and host DNA sequences are giving a better understanding of the evolutionary relationships between different viruses and may help identify the ancestors of modern viruses. To date, such analyses have not proved which of these hypotheses is correct.[58] However, it seems unlikely that all currently known viruses have a common ancestor, and viruses have probably arisen numerous times in the past by one or more mechanisms.[59]

Prions are infectious protein molecules that do not contain DNA or RNA.[60] They can cause infections such as scrapie in sheep, bovine spongiform encephalopathy ("mad cow" disease) in cattle, and chronic wasting disease in deer; in humans, prionic diseases include Kuru, Creutzfeldt–Jakob disease, and Gerstmann–Sträussler–Scheinker syndrome.[61] Although prions are fundamentally different from viruses and viroids, their discovery gives credence to the theory that viruses could have evolved from self-replicating molecules.[62]

And for more on the evolution of viruses:
https://en.m.wikipedia.org/wiki/Evolution_of_viruses

Feel free to ask more questions, though keep in mind I'm not a virologist. :lol:

 

[LLJKSiLk]

I appreciate your answers, and don't worry I'm not a scientist or particularly knowledgeable about this subject at all - but I am interested in science and learning so that puts me a leg up on many people in my state at least.

The hypothesis listed for possible origins is interesting as I've tried to think that whether it qualifies as "life" or not it would follow a similar pattern of natural selection for "survival" for lack of a better term.

Evolution is very intuitive as a concept if you understand it properly, so it makes sense that other mechanisms follow a similar pattern.

As you mentioned, the cold/flu virus types seem to be the most common which follows because of how quickly they can change.

Another question, when it comes to vaccinations/immunization it seems that most vaccines are produced using dead/weak copies of the virus they hope to prevent.

However, some sorts of viruses such as H.I.V. don't seem particularly susceptible to this method as our immune system does not seem to recognize them.

We've spent a lot of money on H.I.V. research, but is there any realistic proposition that we can 'cure' it any more than we can cure the common cold?

By that I mean, how many different avenues do we have in the production of vaccines?

Not sure if that makes sense.

 

[Mr_Wilford]

The hypothesis listed for possible origins is interesting as I've tried to think that whether it qualifies as "life" or not it would follow a similar pattern of natural selection for "survival" for lack of a better term.

It is true viruses follow the pattern of natural selection as they evolve. Anything with a code of DNA/RNA will. This alone is not enough to define them as "alive" though. For example, to be classified as living an organism must, according to wikipedia:

Since there is no unequivocal definition of life, the current understanding is descriptive. Life is considered a characteristic of something that exhibits all or most of the following traits:[49][52][53]

Homeostasis: Regulation of the internal environment to maintain a constant state; for example, electrolyte concentration or sweating to reduce temperature.

Organization: Being structurally composed of one or more cells — the basic units of life.

Metabolism: Transformation of energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life.[49]

Growth: Maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter.

Adaptation: The ability to change over time in response to the environment. This ability is fundamental to the process of evolution and is determined by the organism's heredity, diet, and external factors.

Response to stimuli: A response can take many forms, from the contraction of a unicellular organism to external chemicals, to complex reactions involving all the senses of multicellular organisms. A response is often expressed by motion; for example, the leaves of a plant turning toward the sun (phototropism), and chemotaxis.

Reproduction: The ability to produce new individual organisms, either asexually from a single parent organism, or sexually from two parent organisms.[54][55] or "with an error rate below the sustainability threshold."[55]

Viruses only undergo 5 and, in a sense 7, so they're usually not considered alive. However, note that the article makes a point that life is a descriptive definition, which means one day it could change to include viruses.

Evolution is very intuitive as a concept if you understand it properly, so it makes sense that other mechanisms follow a similar pattern.

Sadly, many don't understand that at all. It's a shame. Personally, I have the problem of being able to think up good rebuttals to creationists but not express them very well. That's why I'm typically a lurker, unless specific topics like chromosome fusion or whales are brought up, as I'm well versed in those areas.

As you mentioned, the cold/flu virus types seem to be the most common which follows because of how quickly they can change.

Not only do they mutate fast, but there are many different strains that cause these illnesses. For instance, a "cold" is a set of particular symptoms caused by a virus. But there are over 200 strains that we know of that can bring on these symptoms. Another reason why it's such a common disease.

Another question, when it comes to vaccinations/immunization it seems that most vaccines are produced using dead/weak copies of the virus they hope to prevent.

Typically. They're cultured in egg yolk, I think, which weakens the virus or kills it all together.

However, some sorts of viruses such as H.I.V. don't seem particularly susceptible to this method as our immune system does not seem to recognize them.

While I'm no expert, I think this may be part of how H.I.V differs from most viruses.

See, if you look at say a Rhinovirus (one of the many cold causing families of virus), it infects a cell by injecting it's RNA into the host cell. IIRC, the RNA is then taken to ribosomes or other cell structures and begin producing more copies, until the cell literally burst from being overfilled with viruses.

H.I.V, however, is what's known as a retrovirus. These use an enzyme called reverse transcriptase to basically "fold" their RNA over on itself, making a DNA strand. This DNA is then inserted directly into the genome of the cell. Here, it may be active and make more viruses each time the DNA is scanned. However, it can lay dormant. And when the cell it infects replicates? That viral DNA, called a provirus, is then passed on to the daughter cells. There, it may become active and start producing viral copies in a cell never even exposed on the outside to the pathogen.

Interestingly, up to 8% of our genome may be made of broken provirus inserts, known as endogenous retroviruses. What's more, you can trace these back to the nested hierarchy of phylogeny, and as such, they are great evidence for common ancestry. More here if you're interested: http://www.talkorigins.org/faqs/comdesc/section4.html

We've spent a lot of money on H.I.V. research, but is there any realistic proposition that we can 'cure' it any more than we can cure the common cold?

There actually might be!

http://www.iflscience.com/tags/hiv-cure

But H.I.V is a totally different game from the common cold. You'd need to make one for each of the 200 strains, and some of these strains, like rhinovirus A, can have up to 99 different variations! There's just too much ground to cover and not enough time. Instead of a yearly flu shot it'd be more like a monthly cold shot! :lol:

By that I mean, how many different avenues do we have in the production of vaccines?

This I really don't know. Sorry

 

[LLJKSiLk]

In any event, that was really great information. It will take me a little time to digest, and I do apologize for taking so long between replies as "real life" job, kids, etc. monopolizes a lot of my time.

Thank you so much for taking the time to narrow down some specific areas I can Google-fu with.

This whole topic came up during one of my morning commutes where I just got to thinking about viruses and realized that I had a lot of unanswered questions to explore and it doesn't seem to come up often in general evolution discussions which I intuitively felt would be related in some way because of how they mutate/spread.

I look at life as a constant opportunity to learn. Very thankful I got into a position where I was ready to!

 

[Mr_Wilford]

No problem!

 

[Laurens]

I found this interesting, and worth a listen

http://www.radiolab.org/story/shrink/

It's an interview with Carl Zimmer, and it talks about the possibility that these things known as "megaviruses" are actually life forms that hypothetically regressed (a clumsy term I know) into performing the same functions as a virus. It covers some interesting questions that you raise in this topic as if the theory is true, some viruses or virus like entities originated from something that we would very much consider alive.