To be specific to our conversation, the issue of understanding the nature of viruses is not trivial. For example, because of the misleading concept of viruses as viral particles, even our host Carl Zimmer, a scholar of viruses, described viruses as “just protein shells that package a few genes.” Obviously, Carl knows that his description of viruses is incorrect and misleading; however, the century-old dogma about the nature of viruses is so strong that it overcomes even the most basic knowledge. And, as I previously discussed (see references in previous comments) entire generations of virologists and other scientists have been victims of this dogma.

Indeed, due the dogma of viruses as virus particles, thousands of scientific articles and books written during the last century contain embarrassing errors that border the pseudo-science realm. Take for example, the following quote from James Watson’s book “Molecular Biology of the Gene” which is highly representative of the modern, scientific description of viruses: “all viruses differ fundamentally from cells, which have both DNA and RNA, in that viruses contain only one type of nucleic acid, which may be either DNA or RNA”. Despite the common knowledge, that within their host cells, the so called ‘DNA viruses’ have both nucleic acids, even James Watson, the eminent scientist, who arguably knew nucleic acids better than anyone, has been a victim of this dogma.

@Ed Rybicki: in regard to squirrel query, I think the problem with the squirrels is not that they cross the road, but that it crosses the road in front of a car; to be fair, the cars have only become part of their environment a few generation ago, so we should give them a break on the IQ issue; I predict that in a few millions years from now, very few squirrels will cross the road in front of a car (for multiple reasons).

And a cunning squirrel is still a stupid mammal.

As for “what is a virus?”, however – that CAN be answered, and has been – and it is not very complicated. I have a number of definitions here (http://www.mcb.uct.ac.za/tutorial/virwhat.html); understandably, I prefer my own…B-)

As for answers to YOUR questions:
1) a liger is a hybrid, so a member of no species
2) mushrooms are neither animal nor vegetable; they are fungi
3) still too low to be smart enough not to cross a road.

Just because the answer to a question is unclear, does not necessarily mean it is an interesting or useful question.

As pointed out by Torbjörn, Carl’s remark on the question whether viruses are alive or not is certainly valuable: you can write an article in Scientific American, if not a book, expanding on it.

Most of the problems and confusion associate with this question are associated with the misleading view about the nature of viruses as virus particles and the evolutionary origin of viral lineages.

Since their discovery more than a century ago, viruses have been identified with the virus particles and defined based on the physical, biochemical and biological properties of these particles (see my comment above and references therein). Because of this misleading concept, the question about the living or non-living nature of viruses has remained in disarray.

For example, after Wendell Stanley crystalized the tobacco mosaic virus (i.e. the virus particles produced by the virus), for which he was generously rewarded, the obvious view was: how can crystalized proteins (that’s how Miller erroneously described the biochemical composition of the crystalized virus) be considered living entities? Or to use a more recent perspective about the nature of viruses, the one posted by Carl a few days ago, if viruses are “just protein shells that package a few genes”, how can they be regarded as organisms comparable to the cellular microbes, such as Bacteria or Achaea?

Similarly, the hypotheses about the evolutionary origin of the ancestral viral lineages are critical in addressing the question whether the extant viruses are living or non-living. For example, if viral lineages originated from ‘genetic elements’ that existed before the origin of the cellular organisms, currently the prevalent hypothesis, or if the viral lineages originated later from ‘endogenous cellular genetic elements’, then defining them as living or non-living is more of a judgment call. That’s because it is not clear at what stage during evolution from simple to complex these ‘genetic elements’ can be defined as viruses. On the other hand, if viruses originated from bona fide cellular species (which everyone agrees that are living ) by reductive evolution as predicted by the fusion model on the origin of viruses (1, 2), then it easier and more intuitive to regard viruses as organisms and, therefore, living.

References

1 Bandea CI. A new theory on the origin and the nature of viruses. J Theor Biol.; 105:591-602, 1983.
2 Bandea CI. The origin and evolution of viruses as molecular organisms. Nature Precedings. 2009.(http://hdl.handle.net/10101/npre.2009.3886.1)

With the recent realization that viruses are the most abundant organisms on Earth and that the repertoire of viral genes exceeds that of cellular species, not to mention the significant role played by viruses in the evolution of their hosts (e.g. more than half of the human genome is composed of endogenous viruses and transposable elements), we can confidently say that Earth is “A Planet of Viruses”. Carl Zimmer, our host, has even written a book about this.

When it comes to planet Earth, the realization that it is ‘round’, not ‘flat’, has been one of the major breakthroughs in human knowledge. Although for most people, even for scientists studying various aspect of our planet, this knowledge is not essential, nevertheless, they recognize and appreciate this knowledge as highly significant.

When it comes to viruses, I would think is it important to know what a virus is. Several months ago, I asked virologist Dr. Robin Weiss the question: “What is a virus Dr. Weiss?” The question was in the context of a comment I posted to Weiss’ review of Carl’s book “A Planet of Viruses” (http://www.nature.com/nature/journal/v474/n7351/full/474279a.html#comment-24322).
For whatever reason, but not unexpectedly, Dr. Weiss did not answer the question. However, I expected that Carl, who is a scholar and a science writer about viruses, would be curious about this question. Probably, Carl did not read my comment and previous papers on the subject (1, 2), or maybe he did not agree with my thesis and that of other virologists (e.g. 3, 4) that the nature of viruses has been misinterpreted ever since they were discovered more than a century ago (metaphorically, that’s more than a hundred years of ‘flat-earth’).

In a recent post, Carl wrote: “Viruses…they’re just protein shells that package a few genes, which they insert into a host cell” (http://phenomena.nationalgeographic.com/2013/02/27/the-virus-that-learns/). I’m sure Carl knows that many viruses have more than “a few genes”; he knows that some viruses have more than a thousand genes, which is many times more than some cellular species. But, I don’t think Carl knows what a virus is.

References

1 Bandea CI. A new theory on the origin and the nature of viruses. J Theor Biol.; 105:591-602, 1983.
2 Bandea CI. The origin and evolution of viruses as molecular organisms. Nature Precedings. 2009.(http://hdl.handle.net/10101/npre.2009.3886.1)
3 Claverie JM. Viruses take center stage in cellular evolution. Genome Biol. 2006; 7:110.
4 Forterre P. Giant viruses: conflicts in revisiting the virus concept. Intervirology. 53:362-78, 2010.

In fact, the virus total is probably even higher than 2x the previous estimate: current sampling methods seem to drastically underestimate the population of small circular ssDNA viruses – which have representatives infecting bacteria / archaea as well as marine and terrestrial plants and animals.

Genuinely a Virus Planet!