Is a virus alive?

[invert_nexus]

Would you say they maybe arose because of horizontal gene transfer between prokaryotes? Would that be a plausible way for them to have come into their own as functional, packaged "information" and structure?

How viruses began is a whole 'nother topic. There are theories galore. And no one knows which one is correct.

One theory is that those transposons mentioned by Roman earlier managed to jump right out of the cell altogether.

How?
Random mutation.

Why?
Because they had to. The mutation that occurred demanded it.

Remember that enzymes function because of their physical structure. Chemical rules apply and are mandatory based upon the environment in which they take place.

 

[Vkothii]

Viruses work because of the way their proteins are structured.

Cells work the way they do because they have structured proteins, too. Cells have other structure than proteins, so do viruses.

]Their proteins work because they have to work that way because of their physical structure.

They're compelled to do what they do, by chemical interactions? There's no control of these interactions by a virus or a cell?

]Their is no choice involved.
Their function is mandatory.

A virus doesn't "choose" to interact with a cell membrane, but it has a functionality (like a battery-powered tool does) that is evoked when it does interact with a cell membrane.
The computer virus analogy is accurate, except we don't use a range of computers, so all the computer viruses are functional only within the current "species" of computers, which is a rather small range.

the viral genome is not alive.

according to who?

enzymes function because of their physical structure. Chemical rules apply and are mandatory based upon the environment in which they take place.

So life is also a set of mandatory chemical reactions?
What about regulation, of gene expression, and regulation of metabolism and other cycles? That's all mandated by chemistry too? That guy who said "Life is just chemistry" was on the nail?
So we could put a bunch of chemicals in a test-tube, and voila: mandatory chemical reactions, and life?

And finally:

Sorry? What does that mean? What criteria are you talking about?

The criteria. That you gave in your definition of life. A virus isn't contained in your definition of life...

Really, so that's what was meant with: "Viruses are even lacking criteria from your own definition."
How come you felt you had to answer the question I asked the guy? I didn't understand his statement. It starts with "Viruses are lacking criteria"(??) then mentions a definition I gave, it's worded a little strangely for my language paradigm - maybe he isn't a native speaker of English?

 

[invert_nexus]

Cells work the way they do because they have structured proteins, too. Cells have other stucture than proteins, so do viruses.

Yes. Cells do. Viruses really don't. Viruses are basically genetic material and a few proteins. Sometimes wrapped in a lipid envelope (due to budding from a living cell).

That's one of the reasons why cells are considered alive while a virus is not.

There's no control of these interactions by a virus or a cell?

Sure there is.
Cells use many molecular devices to control various functions. cAMP is one which has a large number of uses:
http://en.wikipedia.org/wiki/Cyclic_adenosine_monophosphate

But, guess what?
These molecular devices also work on the physical level.

There are two things that always strike home the way that proteins function.

1. Velcro.
2. The way that extension cords, hoses, etc seem to get snagged on every little thing.

A virus doesn't "choose" to interact with a cell membrane, but it has a functionality (like a battery-powered tool does) that is evoked when it does interact with a cell membrane.

Is a battery-powered tool alive?
Spring-powered would be more apt, by the way.

The computer virus analogy is accurate, except we don't use a range of computers, so all the computer viruses are functional only within the current "species" of computers, which is a rather small range.

What does that have to do with anything?
Anyway. A computer virus could certainly exist for a 'species' of computer that doesn't exist, but it wouldn't be very useful... would it?

 

[Vkothii]

A computer virus could certainly exist for a 'species' of computer that doesn't exist, but it wouldn't be very useful... would it?

I find it somewhat puzzling that you query my using an analogy, but then appear to see the point of it..?

 

[invert_nexus]

If that was your point, then it was rather pointless.

Viruses evolve themselves out of functionality all the time. It only takes the mutation of a vital envelope protein (that trimer mentioned above for instance) to completely destroy the virus's ability to enter a cell. Once that happens, you could technically say that the virus is designed for a species of cell which doesn't exist. That is, if a cell with a specific protein in its membrane which would interact with the newly mutated viral protein existed, then the virus would be able to usefully interact with that cell. But, since that cell does not exist (at least not where the virus can get to it) then the virus is basically dead in the water.

Thus, the 'except' portion of your analogy isn't valid.

 

[Vkothii]

Regarding your theory of possible viral evolution:

One theory is that those transposons mentioned by Roman earlier managed to jump right out of the cell altogether.

How?
Random mutation.

What about the sharing of genes by bacteria? Are plasmids the result of random mutation too? Is mutation only ever a random event?
What's your definition of a "random" event? For example, is a shower of rain a random event, is some stranger knocking on the door a random event?
Or is a random event something chaotic, and is a chaotic event different to a random one?

 

[invert_nexus]

Ooh. Some stealth editing.

according to who?

Me.
And, apparently, you.
A genome most certainly doesn't seem to come anywhere close to your definition of life.

So life is also a set of mandatory chemical reactions?

Yup. Basically.
At a low level, that's exactly what it is.

What about regulation, of gene expression, and regulation of metabolism and other cycles? That's all mandated by chemistry too? That guy who said "Life is just chemistry" was on the nail?

Yes.

So we could put a bunch of chemicals in a test-tube, and voila: mandatory chemical reactions, and life?

The right chemicals? You bet.

How come you felt you had to answer the question I asked the guy? I didn't understand his statement. It starts with "Viruses are lacking criteria"(??) then mentions a definition I gave, it's worded a little strangely for my language paradigm - maybe he isn't a native speaker of English?

Because I'm just that kinda dude.
And, it seems pretty straightforward to me.
It seems to me that it's your language paradigm that is wonky.

 

[Vkothii]

The computer virus analogy is accurate, except we don't use a range of computers, so all the computer viruses are functional only within the current "species" of computers, which is a rather small range.

I'll have another go since you didn't see the point first time round:
The computer virus analogy is accurate, but only in a narrow sense, because there is a limited range of hosts (not a diverse range). Computer viruses are otherwise a good analogy, because if they aren't adapted to the range (they're adapted to a non-existent architecture, or machine), they won't work, like in the real world of cells and viral infections.

 

[Vkothii]

So we could put a bunch of chemicals in a test-tube, and voila: mandatory chemical reactions, and life?

The right chemicals? You bet.

What sort of test-tube would be needed, an ordinary glass one would do it?

And if you still happen to be wondering:

You continually amaze me at your ability to misunderstand what people are saying. Do you do it on purpose?

If I do misunderstand something, I say so, and query the person who posted it.
Yes, I pretend not to understand sometimes (I thought this might seem obvious, but no biggie). This is an attempt at button-pushing, I admit.

 

[invert_nexus]

What about the sharing of genes by bacteria?

Could be a possibility.

Are plasmids the result of random mutation too?

Yes.

Is mutation only ever a random event?

Hmmm.
I think so. I suppose there could be some mechanism for inducing a specific mutation, but I'm not sure if this would still be considered a mutation or not.
Mutations are accidents in transcribing.

What's your definition of a "random" event?

Hmmm.
Who woulda thunk that we'd now need to enter a semantic debate about the word 'random'?
I certainly don't think that we could call that random, that's for sure.

Random, in terms of genetic mutation, is, in my opinion, defined by a lack of predictability in the outcome of a transcription.

I.e. you have a codon aaa. This should be duplicated but somehow (there are a large number of mechanisms by which this could occur) the codon becomes aat.
This is a mutation. And it's random because it could have been aag or aac instead.

It's not always entirely random as the various mechanisms by which these mutations occur sometimes limit the possibility for mutation.

For instance, there is the possibility that the original stretch of dna was aaagtc and the mechanism for mutation was that the third a was knocked out of the chain. Thus the new stretch would be aagtc. This would be one functional codon and one nonfunctional codon. Of course, the tc codon would, most likely, have another letter following it.

However, the randomness is increased as the particular mechanism of mutation is also somewhat random. An error in transcription. A free radical damaging the dna. Etc.

For example, is a shower of rain a random event

Hmm.
Somewhat. Weather can be predicted with reasonable certainty over short enough time spans.
However, where each individual rain drop will land can not.

is some stranger knocking on the door a random event?

It can be depending on your perspective.
For instance, if you looked outside and saw some strange dude standing in front of your door with his fist upraised preparing to knock, it would certainly seem to be out of place to say, "that was random" regarding the subsequent knocking. If, instead, he folded up your door like a piece of paper and blew his nose with it, you could rightfully call that random.
Yes?

Or is a random event something chaotic, and is a chaotic event different to a random one?

I'm tempted to say your semantic quandaries are random, but they seem as sure as day follows night.

 

[invert_nexus]

What sort of test-tube would be needed, an ordinary glass one would do it?

Sure.
Plenty of room in an ordinary glass test tube.

The computer virus analogy is accurate, but only in a narrow sense, because there is a limited range of hosts (not a diverse range).

Just as there is a limited range of hosts which a particular virus can interact with successfully?

However, I can see that if there were a more diverse pool of computers out there that computer viruses which aren't functional now might find a home somewhere in one of them.

However, the computer virus analogy really isn't valid because computer viruses don't generally evolve. That is, they copy themselves perfectly. Any changes introduced into a computer virus is introduced by someone purposefully.

However, that has nothing to do with Stryder's original point.

 

[Vkothii]

Yes, thanks for the conclusion.
So it's "true" that computer viruses are an analogy that is only applicable in a narrow sense?

Getting back to the "life in a test-tube" scenario:
How many membranes would be needed, and how would they get populated with the proteins normally present? What about vacuoles. ribosomes, the ER, and other structures?
Or just chuck the chemicals in a glass tt and let them sort it out?

 

[invert_nexus]

Or just chuck the chemicals in a glass tt and let them sort it out?

What do you think?

 

[Vkothii]

[randomness is] defined by a lack of predictability in the outcome...

Yes, an unpredictable outcome, or unpredictability in general, is chaos. True randomness is chaotic (and the semantics are important, I think).

If an event has any expectation then it isn't truly random, but rather probabilistic.
The mutation of a triplet codon can, as you point out, go several ways, but the outcome is constrained by the allowed states, so there is an expectation, and predictability.
Like an expectation that rain will occur (because it has before), or an expectation, if you have a house with a door, that someone will knock on the door.

 

[Vkothii]

just chuck the chemicals in a glass tt and let them sort it out?
”

What do you think?

I think chucking a bunch of chemicals in a test-tube might result in some kind of reaction. But a sustained, self-regulating, respiring reaction that equalled life? Probably not very likely; in fact not at all likely.

 

[invert_nexus]

Yes, an unpredictable outcome, or unpredictability in general, is chaos. True randomness is chaotic (and the semantics are important, I think).

If an event has any expectation then it isn't truly random, but rather probabilistic.
The mutation of a triplet codon can, as you point out, go several ways, but the outcome is constrained by the allowed states, so there is an expectation, and predictability.
Like an expectation that rain will occur (because it has before), or an expectation, if you have a house with a door, that someone will knock on the door.

So.
Do you think that you could go back in time and predict the evolution of the giraffe?
After all, mutations aren't random.

The mutation of a triplet codon can, as you point out, go several ways, but the outcome is constrained by the allowed states, so there is an expectation, and predictability.

You fail to take into account that there are an enormous number of factors. Where, in the huge stretch of DNA, will a free radical knock out a single nucleic acid? Which codon will experience a wobble during transcription? Etc.

There are a large number of mutation mechanisms and a huge number of areas in which mutation can occur and a huge amount of time in which these mutations might occur, etc.
Given this, then mutations are random.
Enough of your semantics.

Yes, an unpredictable outcome, or unpredictability in general, is chaos. True randomness is chaotic (and the semantics are important, I think).

Chaos suggests complexity. Complexity is involved in weather prediction. Weather predictions, more often than not, are not very accurate. Why? Too many factors involved to keep track of.

We should be able to determine the entirety of the universe from a complete knowledge of its past (forgetting about uncertainty for the moment), but we can't. It's far too complex.
Now, throw in uncertainty and it all goes out the window.

So.
Tell me why the definition of random is important to the question of whether or not viruses are alive?

I think chucking a bunch of chemicals in a test-tube might result in some kind of reaction. But a sustained, self-regulating, respiring reaction that equalled life? Probably not very likely; in fact not at all likely.

Especially if they were just thrown in randomly as your strawman suggests.
However, if I wanted to 'cheat', I could just throw in a batch of yeast and say that I satisfied the letter of the contract. Yeast, after all, is nothing but a bunch of chemicals.

However, although we do not, at present, have the knowledge or ability to control such reactions, there exists a method by which various chemicals could be brought together in exacting ways which would lead to a series of controlled reactions which would lead to a conglomeration that could be termed life. We come closer to this every day.

 

[Yorda]

life isn't just black and white, dead or alive... if you want to divide life into different states, divide it into at least 7 states. everything is alive to some degree.

 

[Asguard]

Vkothii

Look its quite easy to work this out
Virus's cant replicate independently of a hoast cell so they are not alive
CELLS (be them bacteria or animal and plant cells) CAN devide and replicate independently of anything else so they are alive

 

[invert_nexus]

Missed a post:

...it codes for several products previously not thought to be encoded by viruses ...mimivirus is not dependent on the host cell genome for coding the metabolic pathways for these products.

Do these proteins function outside of an infected cell?
No.
So, your example is not. An example, that is.
It would fall under the category that Roman already outlined: "Unless you mean a cell infected by a virus?"

You do mean a cell infected by a virus, yes?

Q: Does your car work?
A: Only when I drive it.

Does the sun work?
Does the solar system work?
Does Old Faithful work?
Do you drive any or all of these?

Q: What does a car have to do with viruses?
A: Nothing, it's a meaningless comparison: viruses aren't driven around by humans.

No, but it is made of a multitude of complex interacting moving parts.

You're focusing on the wrong aspect of the analogy.
As usual.

Q: Are viruses evolved?
A: Yes
Q: Doesn't that conflict with a definition of life?
A: No
Q: Why not?
A: What, now you want a lesson on how viruses evolve?
Q: How do viruses evolve?

Sigh.
You're so...
Tiresome.

Viruses evolve by natural selection, Herr Frud. The viral genome experiences natural mutations (a great deal of natural mutations, by the way, due to a crappy transcriptase). These mutations affect the functioning of the various proteins by which the virus operates.

Some of these mutations will prove useful. They are useful because they help the virus replicate itself. Useful mutations persist.

Some of these mutations will be harmful. That is, they will hinder the virus in replicating itself. In general, these types of mutation dwindle.

This, in a nutshell, is evolution powered by natural selection.

Yawn.

 

[ElectricFetus]

life isn't just black and white, dead or alive... if you want to divide life into different states, divide it into at least 7 states. everything is alive to some degree.

QFT (Quote for Truth)... Now if we could just agree what those states are and if their just 7.