are viruses alive

Application Discussion Board

This is your sixth discussion board activity that is not part of the module points. As stated in the syllabus, you will have various discussion board activities that will be based on current events, analysis of scientific articles, podcast reflections and more in order to apply what you are learning in this class to your daily life. This discussion board is worth a total of 15 points and will go towards the application discussion board activities points category.

What will you do:

This discussion board is one of your application discussions and will not count towards your module points. You will have two weeks to complete both parts of the discussion. Please note the two two dates.

Read this article: Are Viruses Alive_ – Scientific American.pdf

Actions

Personal Reply (10 pts):

After you read the article, post on this discussion board by clicking “Reply” on the bottom. Discuss whether you think viruses should be considered living or non-living. Directly reference the article and/or textbook to explain why you are taking the stance that you are. Put some thought into your responses and provide me a thorough answer.

You will have to post your own reply before you can see what your peers have written.

Peer Replies (5 points)

Here is your chance to interact with your peers. Reply to your peers posts and let them know what you think of their answer. Do you agree? Do you disagree? WHY? Please respond to 2-3 of your peers posts. Make sure your responses are thoughtful and grounded in scientific evidence, part of the points for the peer replies will be based on the thoughtfulness of your response. Show me you thought about it and debated both sides of this topic with yourself before replying to your peers!

Netiquette:

Please remember to use proper netiquette here and be kind to one another, even in disagreement. Please reference the netiquette page and the rules for discussion board responses in the orientation module.

You will have two weeks to complete this discussion board. This discussion board assignment will be included in Module 5c and Module 6a. I recommend splitting up the work and doing your personal replies during week one and your peer replies during week two.

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11/8/2020
Are Viruses Alive? – Scientific American
B I OLOGY
Are Viruses Alive?
Although viruses challenge our concept of what “living” means, they are vital members of the web of life
By Luis P. Villarreal on August 8, 2008
Credit: Gopal Murty Getty Images
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Editor’s Note: This story was originally published in the December 2004 issue of Scientific
American.
In an episode of the classic 1950s television comedy The Honeymooners, Brooklyn bus driver
Ralph Kramden loudly explains to his wife, Alice, “You know that I know how easy you get
the virus.” Half a century ago even regular folks like the Kramdens had some knowledge of
viruses—as microscopic bringers of disease. Yet it is almost certain that they did not know
exactly what a virus was. They were, and are, not alone.
For about 100 years, the scientifi c community has repeatedly changed its collective mind
over what viruses are. First seen as poisons, then as life-forms, then biological chemicals,
viruses today are thought of as being in a gray area between living and nonliving: they cannot
replicate on their own but can do so in truly living cells and can also affect the behavior of
their hosts profoundly. The categorization of viruses as nonliving during much of the modern
era of biological science has had an unintended consequence: it has led most researchers to
ignore viruses in the study of evolution. Finally, however, scientists are beginning to
appreciate viruses as fundamental players in the history of life.
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Coming to Terms
It is easy to see why viruses have been diffi cult to pigeonhole. They seem to vary with each
lens applied to examine them. The initial interest in viruses stemmed from their association
with diseases—the word “virus” has its roots in the Latin term for “poison.” In the late 19th
century researchers realized that certain diseases, including rabies and foot-and-mouth, were
caused by particles that seemed to behave like bacteria but were much smaller. Because they
were clearly biological themselves and could be spread from one victim to another with
obvious biological effects, viruses were then thought to be the simplest of all living, genebearing life-forms.
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Their demotion to inert chemicals came after 1935, when Wendell M. Stanley and his
colleagues, at what is now the Rockefeller University in New York City, crystallized a virus—
tobacco mosaic virus—for the fi rst time. They saw that it consisted of a package of complex
biochemicals. But it lacked essential systems necessary for metabolic functions, the
biochemical activity of life. Stanley shared the 1946 Nobel Prize— in chemistry, not in
physiology or medicine—for this work.
Further research by Stanley and others established that a virus consists of nucleic acids (DNA
or RNA) enclosed in a protein coat that may also shelter viral proteins involved in infection.
By that description, a virus seems more like a chemistry set than an organism. But when a
virus enters a cell (called a host after infection), it is far from inactive. It sheds its coat, bares
its genes and induces the cell’s own replication machinery to reproduce the intruder’s DNA or
RNA and manufacture more viral protein based on the instructions in the viral nucleic acid.
The newly created viral bits assemble and, voilà, more virus arises, which also may infect
other cells.
These behaviors are what led many to think of viruses as existing at the border between
chemistry and life. More poetically, virologists Marc H. V. van Regenmortel of the University
of Strasbourg in France and Brian W. J. Mahy of the Centers for Disease Control and
Prevention have recently said that with their dependence on host cells, viruses lead “a kind of
borrowed life.” Interestingly, even though biologists long favored the view that viruses were
mere boxes of chemicals, they took advantage of viral activity in host cells to determine how
nucleic acids code for proteins: indeed, modern molecular biology rests on a foundation of
information gained through viruses.
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Molecular biologists went on to crystallize most of the essential components of cells and are
today accustomed to thinking about cellular constituents—for example, ribosomes,
mitochondria, membranes, DNA and proteins—as either chemical machinery or the stuff that
the machinery uses or produces. This exposure to multiple complex chemical structures that
carry out the processes of life is probably a reason that most molecular biologists do not
spend a lot of time puzzling over whether viruses are alive. For them, that exercise might
seem equivalent to pondering whether those individual subcellular constituents are alive on
their own. This myopic view allows them to see only how viruses co-opt cells or cause disease.
The more sweeping question of viral contributions to the history of life on earth, which I will
address shortly, remains for the most part unanswered and even unasked.
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To Be or Not to Be
The seemingly simple question of whether or not viruses are alive, which my students often
ask, has probably defi ed a simple answer all these years because it raises a fundamental
issue: What exactly defi nes “life?” A precise scientifi c defi nition of life is an elusive thing,
but most observers would agree that life includes certain qualities in addition to an ability to
replicate. For example, a living entity is in a state bounded by birth and death. Living
organisms also are thought to require a degree of biochemical autonomy, carrying on the
metabolic activities that produce the molecules and energy needed to sustain the organism.
This level of autonomy is essential to most definitions.
Viruses, however, parasitize essentially all biomolecular aspects of life. That is, they depend
on the host cell for the raw materials and energy necessary for nucleic acid synthesis, protein
synthesis, processing and transport, and all other biochemical activities that allow the virus
to multiply and spread. One might then conclude that even though these processes come
under viral direction, viruses are simply nonliving parasites of living metabolic systems. But a
spectrum may exist between what is certainly alive and what is not.
A rock is not alive. A metabolically active sack, devoid of genetic material and the potential
for propagation, is also not alive. A bacterium, though, is alive. Although it is a single cell, it
can generate energy and the molecules needed to sustain itself, and it can reproduce. But
what about a seed? A seed might not be considered alive. Yet it has a potential for life, and it
may be destroyed. In this regard, viruses resemble seeds more than they do live cells. They
have a certain potential, which can be snuffed out, but they do not attain the more
autonomous state of life.
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Another way to think about life is as an emergent property of a collection of certain nonliving
things. Both life and consciousness are examples of emergent complex systems. They each
require a critical level of complexity or interaction to achieve their respective states. A neuron
by itself, or even in a network of nerves, is not conscious—whole brain complexity is needed.
Yet even an intact human brain can be biologically alive but incapable of consciousness, or
“brain-dead.” Similarly, neither cellular nor viral individual genes or proteins are by
themselves alive. The enucleated cell is akin to the state of being braindead, in that it lacks a
full critical complexity. A virus, too, fails to reach a critical complexity. So life itself is an
emergent, complex state, but it is made from the same fundamental, physical building blocks
that constitute a virus. Approached from this perspective, viruses, though not fully alive, may
be thought of as being more than inert matter: they verge on life.
In fact, in October, French researchers announced fi ndings that illustrate afresh just how
close some viruses might come. Didier Raoult and his colleagues at the University of the
Mediterranean in Marseille announced that they had sequenced the genome of the largest
known virus, Mimivirus, which was discovered in 1992. The virus, about the same size as a
small bacterium, infects amoebae. Sequence analysis of the virus revealed numerous genes
previously thought to exist only in cellular organisms. Some of these genes are involved in
making the proteins encoded by the viral DNA and may make it easier for Mimivirus to coopt host cell replication systems. As the research team noted in its report in the journal
Science, the enormous complexity of the Mimivirus’s genetic complement “challenges the
established frontier between viruses and parasitic cellular organisms.”
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Impact on Evolution
Debates over whether to label viruses as living lead naturally to another question: Is
pondering the status of viruses as living or nonliving more than a philosophical exercise, the
basis of a lively and heated rhetorical debate but with little real consequence? I think the
issue is important, because how scientists regard this question infl uences their thinking
about the mechanisms of evolution.
Viruses have their own, ancient evolutionary history, dating to the very origin of cellular life.
For example, some viral- repair enzymes—which excise and resynthesize damaged DNA,
mend oxygen radical damage, and so on— are unique to certain viruses and have existed
almost unchanged probably for billions of years.
Nevertheless, most evolutionary biologists hold that because viruses are not alive, they are
unworthy of serious consideration when trying to understand evolution. They also look on
viruses as coming from host genes that somehow escaped the host and acquired a protein
coat. In this view, viruses are fugitive host genes that have degenerated into parasites. And
with viruses thus dismissed from the web of life, important contributions they may have
made to the origin of species and the maintenance of life may go unrecognized. (Indeed, only
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four of the 1,205 pages of the 2002 volume The Encyclopedia of Evolution are devoted to
viruses.)
Of course, evolutionary biologists do not deny that viruses have had some role in evolution.
But by viewing viruses as inanimate, these investigators place them in the same category of
infl uences as, say, climate change. Such external infl uences select among individuals having
varied, genetically controlled traits; those individuals most able to survive and thrive when
faced with these challenges go on to reproduce most successfully and hence spread their
genes to future generations.
But viruses directly exchange genetic information with living organisms—that is, within the
web of life itself. A possible surprise to most physicians, and perhaps to most evolutionary
biologists as well, is that most known viruses are persistent and innocuous, not pathogenic.
They take up residence in cells, where they may remain dormant for long periods or take
advantage of the cells’ replication apparatus to reproduce at a slow and steady rate. These
viruses have developed many clever ways to avoid detection by the host immune system—
essentially every step in the immune process can be altered or controlled by various genes
found in one virus or another.
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Furthermore, a virus genome (the entire complement of DNA or RNA) can permanently
colonize its host, adding viral genes to host lineages and ultimately becoming a critical part of
the host species’ genome. Viruses therefore surely have effects that are faster and more direct
than those of external forces that simply select among more slowly generated, internal
genetic variations. The huge population of viruses, combined with their rapid rates of
replication and mutation, makes them the world’s leading source of genetic innovation: they
constantly “invent” new genes. And unique genes of viral origin may travel, finding their way
into other organisms and contributing to evolutionary change.
Data published by the International Human Genome Sequencing Consortium indicate that
somewhere between 113 and 223 genes present in bacteria and in the human genome are
absent in well-studied organisms—such as the yeast Saccharomyces cerevisiae, the fruit fly
Drosophila melanogaster and the nematode Caenorhabditis elegans—that lie in between
those two evolutionary extremes. Some researchers thought that these organisms, which
arose after bacteria but before vertebrates, simply lost the genes in question at some point in
their evolutionary history. Others suggested that these genes had been transferred directly to
the human lineage by invading bacteria.
My colleague Victor DeFilippis of the Vaccine and Gene Therapy Institute of the Oregon
Health and Science University and I suggested a third alternative: viruses may originate
genes, then colonize two different lineages—for example, bacteria and vertebrates. A gene
apparently bestowed on humanity by bacteria may have been given to both by a virus.
In fact, along with other researchers, Philip Bell of Macquarie University in Sydney,
Australia, and I contend that the cell nucleus itself is of viral origin. The advent of the nucleus
— which differentiates eukaryotes (organisms whose cells contain a true nucleus), including
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humans, from prokaryotes, such as bacteria—cannot be satisfactorily explained solely by the
gradual adaptation of prokaryotic cells until they became eukaryotic. Rather the nucleus may
have evolved from a persisting large DNA virus that made a permanent home within
prokaryotes. Some support for this idea comes from sequence data showing that the gene for
a DNA polymerase (a DNAcopying enzyme) in the virus called T4, which infects bacteria, is
closely related to other DNA polymerase genes in both eukaryotes and the viruses that infect
them. Patrick Forterre of the University of Paris-Sud has also analyzed enzymes responsible
for DNA replication and has concluded that the genes for such enzymes in eukaryotes
probably have a viral origin.
From single-celled organisms to human populations, viruses affect all life on earth, often
determining what will survive. But viruses themselves also evolve. New viruses, such as the
AIDS-causing HIV-1, may be the only biological entities that researchers can actually witness
come into being, providing a real-time example of evolution in action.
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Viruses matter to life. They are the constantly changing boundary between the worlds of
biology and biochemistry. As we continue to unravel the genomes of more and more
organisms, the contributions from this dynamic and ancient gene pool should become
apparent. Nobel laureate Salvador Luria mused about the viral infl uence on evolution in
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1959. “May we not feel,” he wrote, “that in the virus, in their merging with the cellular
genome and reemerging from them, we observe the units and process which, in the course of
evolution, have created the successful genetic patterns that underlie all living cells?”
Regardless of whether or not we consider viruses to be alive, it is time to acknowledge and
study them in their natural context—within the web of life.
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ABOUT THE AUTHOR(S)
LUIS P. VILLARREAL is director of the Center for Virus Researchat the University of
California, Irvine. He was born in East LosAngeles. He received his doctorate in biology from
the Universityof California, San Diego, and did postdoctoral research invirology at Stanford
University with Nobel laureate Paul Berg.He is active in science education and has received a
NationalScience Foundation Presidential Award for mentoring. In his currentposition,
Villarreal has established programs for the rapiddevelopment of defenses against
bioterrorism threats. He hastwo sons and enjoys motorcycles and Latin music.
Scientific American is part of Springer Nature, which owns or has commercial relations with thousands of scientific publications (many of them
can be found at www.springernature.com/us). Scientific American maintains a strict policy of editorial independence in reporting
developments in science to our readers.
© 2 0 2 0 S C IE N T I FI C A ME R IC A N , A D I V IS I O N O F S PR I N G ER N AT UR E A MER IC A, IN C.
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A L L R IG HT S R E SE R V E D .
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