Viruses: Living or Non-living organisms

Ryan_m_b

Hmm however by this definition products of genetic algorithms would be classed as alive.

Moonbear

It's sort of like when I assign final grades in a course, and someone emails me that they are only some smidgen of a percentage point from the cut-off for the next letter grade and pleads for a grade bump. The answer is that wherever the cut-off is set, there will be someone with a grade close to that cut-off, especially in a large course. The same holds for how we define life. In a way, the definitions try to take into account things we have a gut feeling are "alive" but no matter how we define it, something will just miss the cut off and be the topic of this same debate.

The only potential value in defining a cut off for what is alive would be to foist some topics over onto the chemists that the biologists don't want to deal with. Biology is the study of life, so if it's not alive, and it involves chemical reactions of some sort, maybe we can make it the problem of the chemists instead. Of course, in reality, that's why fields like biochemistry exist, and why chemists work on biological problems and biologists work on chemical problems, because again, there's a range of topics that bridge the two subjects and are not easily defined as one or the other, nor do I think they should be.

Pythagorean

Yes! I'm glad you agree with my point! This is not something special about life (or else we would have a clear cut distinction, right? :)

This is the same problem with, say, conductors vs. insulators. There is no perfect conductor or insulator. Everything exists in between (i.e. they are two ideals we have invented for studying them). But we can still identify regions where we say "oh that's definitely not a conductor" (even though electrons do actually move across the substance).

So life will have the same kind of spectrum... but the point is we still have yet to quantify it mathematically; and once we do, we would expect a rock to be at one end, animals to be at the other, and viruses to be somewhere in between.

But the point I was discussing, was whether the measure would be useful or not:

...and I am contending that it would be useful to have a quantitative test for living things. Quantitative classification is always useful to prediction, even if we accept that near the boundaries between regions (living/non-living or conductor/insulator) there are some problems with a rigid definition.

Even in Moonbear's example above, she outlines how the distinctions are useful, even though the boundaries are fuzzy. That's the nature of EVERYTHING we study! Not just life!

fuzzyfelt

Probability?

Ryan_m_b

I addressed this above and I think the point still stands:

dpsguy

I think a mention of Mimivirus would be relevant here.

From the Wikipedia page on mimivirus:


See also the Nature Education article on this topic.

Ryan_m_b

Good thing to bring up, though this would be the relevant part for me:

apeiron

Robert Rosen did argue a mathematical definition of life based on category theory - see his M/R systems, or metabolism-replication, work.

http://planetmath.org/encyclopedia/MRSystem.html

On that score, a virus has the replication but it has to borrow the metabolism - so "borrowed life" is a good way to put it.

This also fits with an evo-devo approach to evolution as clearly a virus evolves quite happily. It has that aspect of life. But it has to borrow its development, the metabolic processes.

This M/R systems definition at least allows you to more sharply separate virus fragments as genetic information from "mere" physico-chemical potentials, the self-organising metabolic cycles that life harnesses.

So maybe rather than being in the middle of the living spectrum, a virus comes from way over one side, an extreme, as a naked stripped down replicator which only evolves.

There are still grey areas of course. Like the 8% of our genome which is retroviral contamination apparently. The line between parasite and host is really getting blurred once the DNA become part of the host's genetic diversity!

http://www.uta.edu/ucomm/mediarelati...st-reports.php

Pythagorean

Interesting metric by Rosen. I can see how a virus would be an extreme by a particular metric; One point to keep in mind is that life probably won't be measured by the dimensionality of one variable, so while an extreme is hit in one dimension by viruses, the landscape across the whole n-dimensional space may have maxima at places other then the extrema of each abscissa.

Pythagorean

Sorry, I missed the context of this. While probability is an important example, even deterministic models have behavior that eludes definitions. In stability analysis, we eventually have to ignore anything beyond first order terms if we want to move forward with conceptual discussion and theory. We can define the behavior for which the eigenvalues of a nonlinear system are positive (repellor) or negative (attractor). But we can't easily talk about what happens when one of the eigenvalues is 0, because those second order terms become important. For each system, we'd have to do the second order analysis (and if that's 0 too, we have to do third-order.. and if that's zero...) and for sufficiently high-dimensional systems, there will be no generalizing of the behavior.

apeiron

Except it is explicitly a two variable model - a dichotomy. So you would have a pair of orthogonal axes. The virus might land entirely on the x-axis (or Replication axis), while an H2O molecule lands entirely on the y-axis (or Metabolism axis). Then living systems would have some co-ordinate on the plane created.

Instead of M-R, I might suggest we use entropy and meaning as purer descriptions. So a virus is all meaning (no entropy, just the constraints), while water is all entropy (no meaning, just the unconstrained material potential).

So a virus would be high in meaning, low if not zero in entropy measured in this two-variable space. Only a handful of base pairs can control a lot of cellular activity. And there is no wasted fat in information terms.

While water is maximally entropic on its own. Or within some cell, it then takes on a distinct temperature and pressure at least. It gains information by becoming part of a cell's organised metabolic economy.

On the other hand, your idea of an n-dimensional phase space doesn't capture the essential distinction Rosen was making. That would be just modelling a system's degrees of freedom, creating as many axes as you think there are degrees of freedom.

The systems approach is instead to measure both the degrees of freedom and their constraints. And Rosen was offering a maximally general model in terms of metabolism and replication, which I am suggesting becomes even more generalised as entropy and meaning.

I've got to say Rosen's scheme never stuck me as fully worked out. In fact, he called it metabolism-repair more than metabolism-replication. He also tried to make a strong connection to anticipation, his anticipatory systems papers. So his was a work in progress, and I'm now thinking that entropy-meaning (the kind of division now being made in biosemiosis) is sharper yet.

This means we still need a metric to define meaning. Another mathematical biologist who I believe is doing good work on this angle is Bob Ulanowicz - http://en.wikipedia.org/wiki/Ascendency

fuzzyfelt

Thank you very much for replying, Pythagorean. I'm very sorry, I thought I had deleted the question, as I was thinking of a different one about subjective probability and multi-valued categories, but hadn't managed to do so, but thanks so much for your help.

Flatland

Perhaps we need a new classification that exists between life and non-life?

Biosyn

Gene Creatures

Amiri Daudi

Viruses are of botanical and zoological enigma.There some facts which shows that they are living and some facts that they are non-living.This is the reason why diseases cause by viruses are difficult to treat the only remedial measure is using the vaccines.The viruses replicate in this respect this is one characteristic of a living thing that of reproduction.On the other hand viruses can be crystalised and kept in a bottle and close even for 300yrs but when release and found their substrate organ they start to replicate again this charactiristic is not in living organisms.Viruses do not respire,digest or excrete as living organisms do.

Ryan_m_b

It's more a case of we don't have a definition that can adequately deal with viruses rather than us not having enough facts about them.
Vaccines are not the only measure and for some diseases there is no vaccine but there are treatments (like interferon or anti-retrovirals). I'm not sure what you mean by difficult to treat as I am unsure what you are comparing it to.
You can also put the component parts of viruses into a vial and they self assemble, in that respect they are complex biological nanoparticles capable of self assembly.

ViewsofMars

The American Society of Microbiology states:

1. A virus is basically a tiny bundle of genetic material—either DNA or RNA—carried in a shell called the viral coat, or capsid, which is made up of bits of protein called capsomeres. Some viruses have an additional layer around this coat called an envelope. That's basically all there is to viruses.

2. Viruses are the simplest and tiniest of microbes; they can be as much as 10,000 times smaller than bacteria. Viruses consist of a small collection of genetic material (DNA or RNA) encased in a protective protein coat called a capsid. (Retroviruses are among the infectious particles that use RNA as their hereditary material. Probably the most famous retrovirus is human immunodeficiency virus, the cause of AIDS.) In some viruses, the capsid is covered by a viral envelope made of proteins, lipids and carbohydrates. The envelopes may be studded by spikes made of carbohydrates and proteins that help the virus particles attach to host cells. Outside of a host, viruses are inert, just mere microbial particles drifting aimlessly.

http://www.microbeworld.org/index.ph...d=77&Itemid=72