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About LinkBacksI'm doing some research in viruses, and this question has always hit me. Should bacteria and viruses be grouped in the same taxonomic category? What do you guys think, and why?
EDIT: I've added a poll.
December 11th, 2007, 07:47 PM
I'm doing some research in viruses, and this question has always hit me. Should bacteria and viruses be grouped in the same taxonomic category? What do you guys think, and why?
EDIT: I've added a poll.
Why would they be grouped in the same category?
Well I'm asking you if they should. I honestly think they should because they both have advantages and dis-advantages. A bacteria causes disease while a virus causes a viral infection (disadvantages). But a virus can also be used to cure stuff, such as cancer. Most bacteria are completely harmless and some of them are very useful. But some bacteria can cause diseases, either because they end up in the wrong place in the body, or simply because they are 'designed' to invade us.
The same line of thought applies to certain types of eucaryotic cells.
Consider various fungal infections and protozoal infections. Helminthic parasites, for that matter.....
Taxonomic organization is not supposed to reflect how useful or harmful different organisms are to humans. They're supposed to represent the phylogenetic - aka, evolutionary - relationship between different organisms. Viruses are substantially different from bacteria and the two lineages probably split relatively soon after life began. It is not appropriate to group the existing species together in the same taxonomic clade.Originally Posted by SmartLeet
Would you put fish and seals in the same group because they both swim in the sea and people use them as food?
Dang, thats a great theory and example. Thanks! But I would like to also hear what other people say.Taxonomic organization is not supposed to reflect how useful or harmful different organisms are to humans. They're supposed to represent the phylogenetic - aka, evolutionary - relationship between different organisms. Viruses are substantially different from bacteria and the two lineages probably split relatively soon after life began. It is not appropriate to group the existing species together in the same taxonomic clade.
Would you put fish and seals in the same group because they both swim in the sea and people use them as food?
Sure, if you want. It's not a theory, though. That's the method used to organize species. It's not exactly up for debate.
You could always start a new system, though, just for the purposes of relating other life to humans. *shrugs*
What paralith said.
To add, here's a nice little summary of some general differences:
http://www.drgreene.com/21_527.html
Viruses are tiny geometric structures that can only reproduce inside a living cell. They range in size from 20 to 250 nanometers (one nanometer is one billionth of a meter). Outside of a living cell, a virus is dormant, but once inside, it takes over the resources of the host cell and begins the production of more virus particles. Viruses are more similar to mechanized bits of information, or robots, than to animal life.
Bacteria are one-celled living organisms. The average bacterium is 1,000 nanometers long. (If a bacterium were my size, a typical virus particle would look like a tiny mouse-robot. If an average virus were my size, a bacterium would be the size of a dinosaur over ten stories tall. Bacteria and viruses are not peers!) All bacteria are surrounded by a cell wall. They can reproduce independently, and inhabit virtually every environment on earth, including soil, water, hot springs, ice packs, and the bodies of plants and animals.
other systems have been tried in the past, but they have all been abandoned as being less useful than the current taxonomy based on kinship : after all, the latter is based on objective reality, Smartleet's proposal (and other, similar ones) on personal preference
The phylogenetic origin of viruses is a tricky subject. They seem to have evolved multiple times independently.
What is clear though is that they cannot be shoved into a meaningful taxonomic group with bacteria unless it is 'organism' or 'Gaeabionta'.
Meaning all life on earth.
which would include you and me also.
Absolutely no way can viruses be grouped with bacteria. We are much more closely related to bacteria than they are to viruses. If you want to group the viruses with anything, group them with prions.
As Spurious observed the only way you can group them with bacteria is if you are going for an all inclusive life forms grouping - and not everyone agrees viruses are even alive.
And as paralith said, this simply isn't up for debate.
Not to mention the way they go about those things... how they effect humans are drastically different. The only similarity, which is very general, is that they infect other organisms and proliferate, usually resulting in harm to the organism.
Absolutely not! The two groups are not phylogenetically related in anywhere near a close enough manner to be grouped together. Your question presupposes that there is some sort of arbitrary choice of assignment; which, at least in the most commonly utilized forms of taxonomy, is patently inaccurate.
Now, the question of whether a virus should be considered "alive" is a different one, the answer to which, in my opinion, is yes.
The only correllation you can make between viruses and bacteria is that they both contain dna, other than that they are totally different. Some bacteria cause sickness, others help us digest our food in our intestines, others float around in the air, live in the ground, or swim in water without ever causing harm to anybody.
Not all viruses will make their host sick, some viruses can infect bacteria. Viruses and bacteria are neither "good" or "bad" they are just opportunistic organisms, or intities (in the case of viruses, for sometime it has been argued wether to even classify a virus as living.)
Classifying Bacteria and viruses into the same category just because a few of each can cause illness is not a good way to classify things.
As a matter of fact, some viruses do not contain DNA at all, and only have RNA.
it seems that a 10th century chinese encyclopedia (probably apocryphal) used the following method to classify organisms :
(a) those that belong to the Emperor
(b) embalmed ones
(c) those that are trained
(d) suckling pigs
(e) mermaids
(f) fabulous ones
(g) stray dogs
(h) those that are included in this classification
(i) those that tremble as if they were mad
(j) innumerable ones
(k) those drawn with a very fine camel's hair brush
(l) others
(m) those that have just broken a flower vase
(n) those that resemble flies from a distance
the fact that this classification strikes us as unusual is because it uses the same approach as proposed by Smartleet : based on perceived utility from a rather parochial point of view
you'll notice that the logic soon becomes unstuck if the sole reason for lumping them together is their ill effect on human beings
I'm going to confirm with you that your right. Some virus' have RNA and are referred as an RNA virus such as flu. So RNA virus' spread on.As a matter of fact, some viruses do not contain DNA at all, and only have RNA.
But do Virus' have anything to do with an increased rate of cancer? Other than just infecting the crazy amount of cells being made in the body uncontrollably?
I don't know about contributing to the increased rate of cancer, but yes, there are cancer-causing viruses. The cervical-cancer causing viruses are getting particular attention lately, and there are several others, including viruses that cause leukemia.I'm going to confirm with you that your right. Some virus' have RNA and are referred as an RNA virus such as flu. So RNA virus' spread on.As a matter of fact, some viruses do not contain DNA at all, and only have RNA.
But do Virus' have anything to do with an increased rate of cancer? Other than just infecting the crazy amount of cells being made in the body uncontrollably?
Haha, you got pwned. But Seriously, I do not think that Bacteria should be in the same category as Viruses. Just wanted to add my two cents =]
If Viruses and Bacteria become grouped together then I think that all animals that can live in a house, should be classified together too. =P
Agreed, viruses are totally different from bacteria.
* different ways of carying genetic data
* different way to feed
* different way to multiply
* and much more ....
... every single thing is different[/list]
March 18th, 2008, 08:44 PM
And then there's the prions, which are entirely proteinaceous viruses, no nucleic acid at all, but there's debate as to whether they should be classed as "viruses" or some new classification of infectious organisms.
I go with this: the Journal of Virology publishes papers about prions. They must be viruses.
And there's more particles after infection than before, so they can't be classified as a toxin.
TK
March 21st, 2008, 06:57 PM
I don't agree because prions can develop spontaneously in people as in type one Creutzfeldt-Jakob's, a virus is much more complicated than a prion. A virus replicates itself, but I've always thought of prions as just misfolded proteins that are resistant to degredation and have the nasty affect of altering the conformation of other proteins too, after all they can't replicate themselves all they can do is change other proteins into prions. Viroids are another tricky subject, but don't get much coverage because they have only been identified in plants. They are just circles of RNA similar to plasmids that lack a protein coat.
Edit: I do agree that they aren't a toxin, maybe they are just unique.
Adding viruses to bacteria would be just plain wrong...
structures are pretty different,
and it is still arguable whether viruses are living or not...
Pretty different is an understatement.
And yet the Mimivirus was classified as a bacterium till not so long ago.
http://www.journals.uchicago.edu/doi/abs/10.1086/518608
Clinical Infectious Diseases 2007;45:95–102
I've been reading up on the evolution of life today and I think most of us are still filled up with the cliches generated several decades ago. And this thread is a reflection of that.While characterizing a collection of bacteria that had been isolated using this approach, we encountered an organism that, on preliminary analysis, appeared to be a gram-positive coccus. However, additional examination revealed that it was not a bacterium but rather, surprisingly, a virus. The dimensions of the virus particle (diameter, 0.8 μm) and its genome size (1.2 Mb) are far more akin to those of bacteria than to those of previously recognized viruses. These characteristics, together with such features as the breadth and complexity of its gene content, challenge the current definition of a “virus.” Furthermore, the virus, now named “Mimivirus,” has been implicated as an agent of pneumonia in humans and, thus, should be considered a putative emerging pathogen.
The discussion is actually going toward such remarkable things such as viruses actually introducing DNA to cellular life, and viruses being the representatives of a fourth group (besides Eubacteria, archea, and eukaryotes) that is now extinct.
So maybe the opening post wasn't that crazy:
with the remark that bacteria should be rephrased as the fourth extinct group of life.
The Mimivirus is remarkable as a virus, but it is hardly a bacteria. It would take quite a stretch for someone to classify it as a bacteria, suggesting that it may be a new Domain, or have a role in the origin of life is fair. Its only similarity to bacteria is the size of the genome and capsid. It still lacks ribosomes, response to stimuli, and homeostasis. Moreover, the reason Bacteria are classified as bacteria is because they all share common physiological properties and similar rRNA genes, which the Mimivirus does not have.
Sure. That is why it was classified as a virus and that is why the reviewers demanded that its genome was fully sequenced, which is not a standard request. Because it is an obvious virus?
Yeah right. It wasn't a stretch at all. Real experienced researchers HAD classified it as bacteria.
This is really interesting. And after the initial introduction, they might have helped with the spreading of new strands of DNA across both within the same "species" and between different ones. They could have been an accelerating agent in the initial diversification, etc...The discussion is actually going toward such remarkable things such as viruses actually introducing DNA to cellular life, and viruses being the representatives of a fourth group (besides Eubacteria, archea, and eukaryotes) that is now extinct.
They had classified it as a bacteria because it retained the gram stain, most viruses are not visible under light microscope so they made an assumption. After verification they concluded that it was a virus. You can't base an argument on preliminary assumptions, taking into consideration what we now know about the mimivirus, it is an obvious virus. (Though remarkable, maybe it shouldn't be classified as purely a virus, but it shouldn't be a bacteria either.)
Sure. That is why it was classified as a virus and that is why the reviewers demanded that its genome was fully sequenced, which is not a standard request. Because it is an obvious virus?
Yeah right. It wasn't a stretch at all. Real experienced researchers HAD classified it as bacteria.
You fail to recognize the fact that it was unprecedented. And hence not obvious.
And the novelty of mimivirus led to a redefinition of the classification of life in this article:
http://www.nature.com/nrmicro/journa...micro1858.html
read my full synopsis here:
http://spuriousforums.com/viewtopic.php?f=10&t=3611
or in short for you:
The existence of mimiviruses and other discoveries led to the proposal that life should be re-classified into two groups: ribosome-encoding organisms (REO), better known to people as cellular life, and capsid encoding organisms (CEO), better known to people as viruses.
REOs are organized into three main groups: archea, Eukarya and bacteria.
Interestingly CEOs, as they exist today could well be the remnant of an extinct fourth group (as in they are not cellular any more in the classic sense) that didn't share the ribosome encoding machinery with the other three groups. That is Archea, Eukarya and bacteria share a Last common ancestor which is not shared with viruses.
Sounds fascinating. But is the capsid thing cladistically reliable? Suppose it is a symplesiomorphy of all life, then we couldn't tell whether or not viruses as we think of them today are:
1. An early offshoot, prior to REOs, which therefore deserve to be included in the scheme you describe, or
2. Are 'lifestyles', like lichens, say, whereby any living organisms/lineage could adopt a non-metabolic parasitic lifestyle and revert to the capsid form.
Any thoughts/evidence etc?
It involves quite a bit of speculation, especially since the question of whether a virus is alive or not is still controversial. Theories of virus evolution involve multiple cases of evolution from cellular life, devolution of cellular life, or co-evolution along with the earliest cellular life.
The problem everyone has is that viruses have such a high mutation rate that the genetic diversity seen in viruses is overwhelming. Moreover, they leave no fossils.
The question whether a virus isn't really controversial other than that our culture is still pervade with old thoughts.
The notion that a virus isn't alive is a reflection of an old school of thought, not reality. That is, the idea that cellular life is alive and hence life that lacks characteristics typical of cellular life isn't alive.
Hence you automatically reach the conclusion that a virus isn't alive since your criteria for life are based on one group of life.
traditionally (as in molecular) the tree of life has been based on ribosomal DNA. Obviously you are not going to find viruses with that. Especially not if viruses are derived from a fourth group of cellular life that never had ribosomal DNA to start with.
Basing your definition of life on cultural ideas isn't really the way to go forward in science.
I define life as something which maintains homeostasis in an active fashion. No viruses do that, it is the destinction between including all things which are self replicating into the definition of life, or only those which are actively involved in not only self replicating but maintaining their existence.
so in principle this sort of definition could mean that life, by simplifying its functions to the bare necessities for existing, could revert back from being life to being non-life ?
If it simplified its functions to the point where it was no longer expending energy to keep itself alive (at some point in its development), then yes I suppose so. Afterall, we have bacteria which have regressed to the point where they are completely dependent on their host for survival, yet they are still maintaining homeotic stability so they are still alive. All things traditionally defined as alive have mechanisms to react to unfavourable changes in environment.
To have a meaningful definition of life you have to include all life.
Basing the definition of life on cellular life only, and then claiming non-cellular life is not alive is a wasted intellectual effort and unscientific.
I'm sure you have the old guard behind you, but applying logic is more important here I think.
You don't find viruses on mars. Viruses do not come into existence spontaneously. Viruses have been an essential part of life since the very beginning, or close to the very beginning.
And they have continued to be so.
They share the ancestry of life, from crude self-replicating molecules to increased complexity of replication and diversity.
Any meaningful definition of life has to span all life. A definition of cellular life is merely a practical one. To distinguish viral life from cellular life.
Damn! I actually managed to vote "yes" when I was going to vote "no". I hate it when my mind "glitches" like that!
I believe viruses are a product of life, along with prions, viroids, and plasmids. They are not themselves life, just because something is created from life does not make it alive. There are self-replicating clays that show inheritance of structure, but very few people would consider a bed of clay alive. It is undeniable that virus share an intimate origin with cellular life, but if they evolved seperately is uncertain.
That's belief, not science.
Belief based in science, it is inconclusive whether viruses shot off from living organisms from transposons, mutations, or from loss of function, or if newer ideas of extinct non-ribosomal life was their origin.
Provide a definition of what makes viruses alive, is it their capacity to replicated? If so then clays are alive. Is it their genome? Then are viroids and plasmids alive? Clays also show inheritance, although not through nucleic acids. RNA has been shown to be capable of enzymatic activity, it could theoretically self replicate itself, would that RNA then be alive also?
Is your armpit alive?
As an entity no, but it's made up of living cells. o.O
I agree with paralith, this is bogus. The organization of species is not done by effects, behaviors, functions...or even the idealogical labels of human society.
Further, there are huge differences between bacteria and viruses. Reproduction and structure are two big ones.
If we consider that "alive" means replication alone, then maybe yes. However, I don't think we do. Viruses don't really do much except perform perpetual acts of replication, no different from similar functions in cells (or even in machines). I'd argue that viruses are utterly not-alive because of this.
Technically yes...but I doubt it's going to sprout a consciousness and its own reproductive capabilities anytime soon. :P
So it isn't alive.
So your definition stinks.
How so? An armpit is just a part of the body, the tissues that make it up are alive and are variable. Moreover, as a whole the human body meets my criteria of life. We as humans attempt to maintain homeostasis through food, hydration, and temperature regulation. So animals, plants, fungi, bacteria, protist, and archaea meet my description. Viruses do not meet that criteria.
I'd like to learn more about this self-replicating clay, i_feel_tiredsleepy. Do you have a link handy?
"Clay theory
In simplified form, clay theory runs as follows: Clays form naturally from silicates in solution. Clay crystals, as other crystals, preserve their external formal arrangement as they grow, snap and grow further. Masses of clay crystals of a particular external form may happen to affect their environment in ways which affect their chances of further replication — for example, a 'stickier' clay crystal is more likely to silt a stream bed, creating an environment conducive to further sedimentation. It is conceivable that such effects could extend to the creation of flat areas likely to be exposed to air, dry and turn to wind-borne dust, which could fall at random in other streams. Thus by simple, inorganic, physical processes, a selection environment might exist for the reproduction of clay crystals of the 'stickier' shape.
There follows a process of natural selection for clay crystals which trap certain forms of molecules to their surfaces (those which enhance their replication potential). Quite complex proto-organic molecules can be catalysed by the surface properties of silicates. The final step occurs when these complex molecules perform a 'Genetic Takeover' from their clay 'vehicle', becoming an independent locus of replication - an evolutionary moment that might be understood as the first exaptation.
Despite its frequent citation as a useful model of the kind of process that might have been involved in the prehistory of DNA, the 'clay theory' of abiogenesis has not been widely accepted."
http://en.wikipedia.org/wiki/Graham_...th#Clay_theory
The heritable nature of the formation of clays has been observed for a long time, it is also a popular, yet not widely recognized, model of how abiogenesis could have occured.
Thanks!
Wow I can't vote I don't even think Virus fit in taxonmy because I don't think there living things they are one of the limited examples of inorganic biology
Taxonomy covers all things capable of being classified, not just animals and plants.
Not when classifing living things I suppose they could be in the same group of things that harmed us i.e. the group that are made of organic compounds
Taxonomy applies to everything, not just "living" things. If you're going to scientifically group something, that's taxonomy.
There is no such group. We do not classify by effect on humanity.
If simply an organic compound, they fall under chemistry, and would be classified under one of the groups of organic compounds.
A new class could always be invented, because taxonomy is meaningless anyway lol. It's just a useful way to organise things, and a way for people to waste time.
I disagree. Certain classifications as they currently stand are probably fairly meaningless, but that's more of a result of their age than of the purpose of taxonomy. Scientific classification/taxonomy should, as best as possible, reflect functionally separate lineages. As a functionally distinct lineage, be it one of life or non-life, viruses can be assigned to a meaningfully distinct class.A new class could always be invented, because taxonomy is meaningless anyway lol. It's just a useful way to organise things, and a way for people to waste time.
Things within a taxa should be linked by a unifying quality, often times in a biological sense this means a single lineage because the quality is conserved throughout evolution, but two things having a related lineage doesn't make them the same taxa. Nonetheless, Linnaean taxonomy has its uses in categorizing related organisms. If viruses evolved from life from transposons or some other form of loose DNA/RNA, then they would have a related lineage to life, but they do not necessarily have all the characteristics necessary to be defined as life. Taxonomy is still largely arbitrary though, you can just keep going to higher levels of order until you include everything in the universe. Or, you could selectively base things on the smallest characteristics until a taxa includes only a handful of organisms.I disagree. Certain classifications as they currently stand are probably fairly meaningless, but that's more of a result of their age than of the purpose of taxonomy. Scientific classification/taxonomy should, as best as possible, reflect functionally separate lineages. As a functionally distinct lineage, be it one of life or non-life, viruses can be assigned to a meaningfully distinct class.A new class could always be invented, because taxonomy is meaningless anyway lol. It's just a useful way to organise things, and a way for people to waste time.
Bacteria are living, viruses are not living.
Viruses do not move, eat, sleep, or reproduce by themselves (They can only reproduce with a host cell). They sort of just "float" around until they are able to attach to a host cell. If they are not living then how do they attach to their host? If I have a pile of keys and throw them at a door, eventually one will go into the keyhole, which is kinda how viruses work with cells, shoot enough viruses at the right cell, and eventually one will attach.
Bacteria get their own energy, repair themselves, and reproduce. Bacteria also react to stimuli and have cell-like features such as cytoplasm, organelles, and cell wall.
One reason that may be able to support that viruses are organisms is that they reproduce. If you look at them it seems that they may have better adapted to attaching to their host with time, or natural selection. Also they have nucleic acids, which every organism has as well.
The study of biology is the study of life. Studying viruses is under the discpline of biology, not any other subject. If it was abiotic, studying viruses would fall under the discpline of chemistry.
Raymond K, once in contact with the appropriate host, a virus does use a mechanism to inject or bore into it. That's a little more active than tossed keys. Well, just a little.
I think the emotions owe to our distaste. Viruses are primally nasty aliens and we don't want them in our club. You could find similar vehemence in a debate whether the giant Alaskan malamute is dog or wolf.
Nice one. I said something similar in a different thread.
Didn't realise you blogged (doh! Doesn't everybody?). Will bookmark.
So does the virus use energy to inject it's DNA into the host cell? Or is it just diffusion?
Most methods of virus entry aren't understood and it changes depending on the group, it involves mostly conformational changes or endocytosis for the most part, it is all spontaneous though or requires the cell to actively take the particle in.So does the virus use energy to inject it's DNA into the host cell? Or is it just diffusion?
People don't seem to understand my viewpoint of viruses, they are definitely biological, but I view them more in the way I would view a single enzyme complex, or a chromosome. They are an aspect and product of life, thus should be studied by biologist, but are not in and of themselves life.
Stamps are part of the postal system. <- not a great analogy.
If viruses are to be included in phylogenies on the basis that their genetic sequence can inform us of their evolutionary history, then plasmids and transposons should be included as independent entities within phylogenies as well.
And?
is there a problem with that?
They already have a specific name, hence they are already classified as distinct units.
Well, I'm currently reading (actually re-reading, but I'm not ashamed) Dawkins' The Ancestor's Tale and he makes the case for considering taxonomy as much along the lines of individual genes themselves, as for the organic lineages in which they're present.
So maybe those are areas we ought to be thinking about. After all, the point about taxonomy is that it should help us in our research and understanding, not that it should (any longer) conform to some pre-Linnaean 'Tree of life'. No?
Plasmids and transposons confer properties upon their hosts, do not survive outside of their host (generally speaking), and their effects upon their host (biological as well as genetic) are already accounted for in present schemes.
If a plasmid or transposon were to be considered a separate entity (which is doubtful given the symbiotic nature with which it exists with its host) then individual chromosomes might as well be considered separate entities (as they can occasionally behave independently from one another over evolutionary history.)
Such an approach may provide a quite nice mathematical framework for following changes in genetic information over time, and may have some use, a use which may be quite grand. Still, such a use would not necessarily generally help achieve the fundamental goals of phylogenetics, which is to descibe relatedness between organisms. I don't believe it is useful either for the layman or for the biologist. I may be entirely wrong.
Everything can be classified into one of two things: those that fit into a classification system you like and those that do not fit into a classifcation system you don't like. (Apart from the obvious exceptions.)
The only way I can think of to classify Viruses and Bacteria should be classifed in the same group is they both are have DNA and/or RNA, harm living things Bacteria even harm themselves and Virsus harm ever living thing no natrual virsus is benefical to the host because they are very insifsticated parsites they don't even try to keep the host alive and Bacterial waste harms us in the wrong place well most of it anyway (I am pratical to vitamin K myself) But since there methods are completly diferent I would put bacteria with toxin producers and Virsus with Carsogenes because it is actually a pretty simlar process when you think about it wow this is getting long and off topic from what everyone else has been saying
That would be a completely arbitrary taxonomy... Moreover harmful entities are already classified under the title of "pathogen".
All those descriptions you provided apply to all organisms, and there are plenty of bacteria that are beneficial to their host.
Yes but that includes far more fungi then that frist guy was taking about
So what if the theory is correct that viruses gave the currently existing cellular life their DNA.
Did they harm them?
[spam deleted]
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