Defining Life: The Debate Over Whether Viruses Qualify

[kuzao]

@ dave
while we seem to agree on the answer our way of coming ot that conclusion seem to be different.

no offense meant but could it be that it is a while ago since you studied molecular biology?

as for transcription and translation, i used these as biological terms. they are defined as coppying dna to rna and then making poly peptides out of rna.
this means that there are actually no artificial 'things', entitys or what ever who translate and transcribe.

@ jungle beast

im not aware of any organism who doesn't contain dna. could you find the name? I am curious.

Understanding the function of DNA makes it obvious that DNA itself is not necessary for life. It's role is simply to store information in a way that can be copied to allow evolution to occur. DNA is certainly not the only molecule that could potentially fill this purpose.

first: of course its not the only molecule but its is certainly the only for EARTH based BIOLOGICAL (some call it organic) life. and that was as, dave pointed out, exactly what i said. are we trying to define what we have here based on 'hard' definitions or are we trying to be philosophical? there is nothing wrong with that, but then the defintion would be so much longer and 'softer'.



second: again there is no offense meant when i say: you didnt had any molecular biology classes, or?
boomboom is right when he says that dna's task are many and not limited to only storing information. expression regulation by dna folding, dna binding and many more ways is big topic in mole. bio.

i do not totaly agree with boomboom on his 'central dogma' theory.
yes it MIGHT. but it might also NOT. we can't say and i proclaim we will never find out because that would require to locate and analyse ALL life (and i mean ALL! not only on Earth or in this galaxy) hencefore this is a irrelevant point and futile to discuss.


one thing we should have a common understanding of is the term 'definition'. do we want something which desribes the essence, the principle of life or do we want a definition as lawyers tend to make them ^^ loooong, wound in strange shape so that every possible and impossible exeption is included and useless? (this time the offense to lawyers is intended :P )

alex

p.s. sry for the typos. being dyslexic AND tired is fatal ^^

 

[DaveC426913]

as for transcription and translation, i used these as biological terms.

Which is a circular argument.

Basically your argument boils down to "life is that which performs biological functions".

 

[DaveC426913]

How can you be so certain? The "central dogma" could very well be universal...across the universe. Until we actually find extraterrestrial life, the words "almost certainly" has no substance to it whatsoever.

Because amino acids can form a nearly infinite variety of proteins. For DNA to arise the same twice - let alone common - is astronomically unlikely.

Personally, I think it will be very similar, but not the same.

 

[kuzao]

@dave

oh far from beeing true. my statement could be read as 'life is what is based on these two functions' (still doesn't sound flashy)

one could see it as a circular argument IF these were the only functions present in organism and thus they could be called the only biological functions.

maybe i should have explained more.
transcription and translation are terms closely realted to presence of rna and dna. thus saying transcription and translation is defining life means presence of dna and rna is defining life.

does this make it more clear to you? do you see now that this is not a 'soft' argument but a very ahrd one? and also not a circular one?

 

[kuzao]

Because amino acids can form a nearly infinite variety of proteins. For DNA to arise the same twice - let alone common - is astronomically unlikely.

Personally, I think it will be very similar, but not the same.

first i think its futile to find a defintion for something we don't even know about yet. that's just discussing because we like to read our on writings...

however i agree on the point that it is unlikely. to be exactly the same. but how exactly the same does it has to be to be still called dna? what if it incorporates uracil instead of thymine. could i then still be called dna?

i assume dave then would argue that its not the same thus he was right while boomboom would say hey look it basically the same?

lets don't wander into that realm. there is no merit there.

 

[DaveC426913]

@dave

oh far from beeing true. my statement could be read as 'life is what is based on these two functions' (still doesn't sound flashy)

one could see it as a circular argument IF these were the only functions present in organism and thus they could be called the only biological functions.


maybe i should have explained more.
transcription and translation are terms closely realted to presence of rna and dna. thus saying transcription and translation is defining life means presence of dna and rna is defining life.


does this make it more clear to you? do you see now that this is not a 'soft' argument but a very ahrd one? and also not a circular one?

No and no.

Translation and transcription do not define life. There are non-living things that translate and transcribe that have nothing to do with DNA or RNA. It is too general.

Your argument is the equivalent of:

All cars have motors. Therefore, the definition of a car is that which has a motor.

 

[kuzao]

as i said before transcription and translation are terms of molecular biology and in this context i used them.

do you understand what translation and transcription means?

there are no things which can translate and transcribe and are artificial (at least to my knowledge and if you don't purposly trying to ridicule my argument by saying that a vial where you put in some dna, rna, polymerase and other things should then be called life)

your car argument is a faulty one. if you understand the meaning of transcription and translation you will understand that all things which inherit these two abilities are life. while not all things inhereting a motor are cars.

if you define life via rna and dna or translation and transcription you will as a result get all the things who can 'do' the 'things' most people asscociate with life. like proliferation, metabolism and so on. which is in my opinion a reason to chose this defintion because it avoids to define something by some 'effect' but instead defines by source / reason.

alex

 

[DaveC426913]

as i said before transcription and translation are terms of molecular biology and in this context i used them.

OK, so let's make that context explicit.

"Life is that which performs biological transcription and translation."

That is circular.

 

[kuzao]

we are talking about viruses and life here of course taht implies that we talk biology here.

do you realize that transcription and translation are synonymes for the presence of rna and dna?

how can chosing the two elemental functions of an organism as lifes definition be a circle argument?


if your point would be valid that woul mean that you need life to define transcription and translation. but you dont.

translation and transcription are chemical processes. you do not have to use 'life' to define them. so how can this definition then be a circular argument?

by the way i feel sorry for the other discussion participants because we take up to much space. should we continue this conversation in skype or via email?

alex

 

[BoomBoom]

i do not totaly agree with boomboom on his 'central dogma' theory.
yes it MIGHT. but it might also NOT. we can't say and i proclaim we will never find out because that would require to locate and analyse ALL life (and i mean ALL! not only on Earth or in this galaxy) hencefore this is a irrelevant point and futile to discuss.

Well, I wasn't claiming that is was for sure, I was making the point that it could be...in order to counter the assertion by JB that it is "almost certain" that DNA from another planet would be different.

The true answer is we don't know, nor can we know until we find some...then we could start to make some educated assumptions perhaps.

 

[kuzao]

totally agreed :)

 

[DaveC426913]

we are talking about viruses and life here of course taht implies that we talk biology here.

We are trying to define life. That means we cannot refer to life processes as definors.

do you realize that transcription and translation are synonymes for the presence of rna and dna?

Only in a biological context. And an Earth biological context at that.

All I am requiring is that you create your life definition without referring to life processes in doing so.

if your point would be valid that woul mean that you need life to define transcription and translation. but you dont.

Transcription is the process of copying something from one medium to another.

Translation is more broad, and involves moving something from one place to another, and several other definitions.

If you wish to further define or qualify those, do so. If you qualify those words in the context of the very thing we are trying to define, you will end up with a circular argument.

translation and transcription are chemical processes. you do not have to use 'life' to define them.

Now you're getting closer to a valid definition. You've removed the reference to biology (life - the circular reference), and are defining it on terms of chemistry. That is not how you were contextualizing it previously.

That is what I was asking for.

"Life is that which performs chemical transciption."

by the way i feel sorry for the other discussion participants because we take up to much space. should we continue this conversation in skype or via email?

They are quite capable of jumping in when and if they wish. It's not like walkie-talkies, where they have to wait for us to finish.

 

[kuzao]

ok maybe i assumed too much.

let me make it absolutly clear: whenever i talk about translation and transcription i mean the biological transcription and translation which is a) copying dna to rna and b) rna to poly peptide.

i thought evrybody realizes that these are chemical processes which can even be done invitro. thus i was bewilderd by your staement that this is a circular argument.



and i stated before that i only talk about Earth and biological life.


to explain what an airplane is can you use wings? i believe you can because you can explain what wings are and then say that an airplane is a thing with attached wings. if however you only say in the first place wings are the things attached to an airplane and then in the second step that an airplane is a thing with attaaeched wings that would be plain stupid.

but you can explain the whole matter by saying tha wing are surfaces generating lift utilizing bernoullis principle. i believe that is the way i try to explain life. i do not use life to define transcription and translation. hence i say that the presence of dna and rna or transription and translation are a nice compact definition of life. (assuming you know what is translation and transcription)

in molecular biology or gentics or biochem or biotech you do never call transcription or translation chemical because these processes take place in the cell and are thus biochemical or by comon agreement 'biological'

so i would say

life is what performs transcription and translation


alex

 

[DaveC426913]

ok maybe i assumed too much.

let me make it absolutly clear: whenever i talk about translation and transcription i mean the biological transcription and translation which is a) copying dna to rna and b) rna to poly peptide.

You could have made it absolutely clear by putting it in your definition anytime after post 52!


It's not that I didn't understand your point, it's that it doesn't make it a definition. Definitions narrow generalities.

 

[kuzao]

as for transcription and translation, i used these as biological terms. they are defined as coppying dna to rna and then making poly peptides out of rna.
this means that there are actually no artificial 'things', entitys or what ever who translate and transcribe.

i belived i made it clear in post 62. i guess i was wrong. sry for that. :)

i see the short commings of this definition my self. there can or better there could be exceptions but i still think this is a good starting point and defines life in its essence (but may be not in total... still curious about the organism which is supposed to contain no dna...)

 

[CRGreathouse]

let me make it absolutly clear: whenever i talk about translation and transcription i mean the biological transcription and translation which is a) copying dna to rna and b) rna to poly peptide.

life is what performs transcription and translation

So life is that which

• Copies DNA to RNA
• Copies RNA to polypeptides

So a virus, which performs neither, is not alive by your definition. A genetics lab which performs ligation and transcription would be alive.

 

[sokrates]

So life is that which

• Copies DNA to RNA
• Copies RNA to polypeptides

So a virus, which performs neither, is not alive by your definition. A genetics lab which performs ligation and transcription would be alive.

Great post.

Very well put after all that hullabaloo.

 

[kuzao]

as i said before you could take this definition and ridicule it by using it for something like a vial where you put the nececary agents in.

this however would be same as finding a definition for an airplane and then trying to ridicule that definition by carying around all the neccecary parts of an airplane and saying here see its not flying...


yes a virus would be not alive (this by the way a view shared by most of the scientific comunity to my knowledge).

what is a genetic lab using to do these tasks?

one of the most delightfull things my chemical analysis prof. said once was: no scientist however mighty or smart he/she might be can perform an analysis with a hplc or a transformation with a lab. he might however use pipets vials gloves solvents coulmns hplcs restrictionenzymes agents etc...

so who in you example is performing the tasks you mentioned? i am pretty sure there is not a single lab in the world which can perform excersion interagtion ligation translation transformation or any other gentic task. there might be however many labs which use certain ezymes and agents do this.

lets ask ourself how these things are done?
i think the answer is by using small little helpers extracted from living organisms or viruses to modify, analyse and alter organsims or generally perform microbiological tasks.

is this making the devinition i suggested before invalid? i do not thing so.
similar you could say the definition is invald because i live but do not know how to transcribe.

alex

 

[DaveC426913]

A genetics lab which performs ligation and transcription would be alive.

This argument could apply to anything you want.
"Life makes copies of itself."
"A lab can do that so it must be alive."
I think it's safe to say that "a bunch of humans performing roles that model the mechanisms of life" is disqualified as being an example of life itself.

 

[Phrak]

DaveC, what's your definition of life? This is very long thread, so if you stated it already, it's worth repeating.

Mine had been: A self replicating, adaptable system.

This leaves out crystals, and includes viruses. I'd want to have prions in the ambiguous middle, but it excludes them entirely.

Edit: The time was getting late. That should have been
A self-similar replicating, adaptive system.

 

[CRGreathouse]

This argument could apply to anything you want.
"Life makes copies of itself."
"A lab can do that so it must be alive."
I think it's safe to say that "a bunch of humans performing roles that model the mechanisms of life" is disqualified as being an example of life itself.

I would expect that most definitions of life would not apply to a genetics lab. For example, genetics labs don't self-replicate; I consider self-replication a requirement for life.

 

[kuzao]

but self replication is quite dangerous that would leave all strile organisms out of the definition so many crops would count as life anymore so many sterile organisms etc tehy can only grow on their own thei can't replicate.

you could get around that at least a bit by saying you apply the definition only to cell sized entitys but still i would say excluding annything what can't grow anymore is a bit difficult

 

[sokrates]

This argument could apply to anything you want.
"Life makes copies of itself."
"A lab can do that so it must be alive."
I think it's safe to say that "a bunch of humans performing roles that model the mechanisms of life" is disqualified as being an example of life itself.

After all those useless points (circular arguments, discussions on semantics, stating big remarks on how definitions narrow generalities), is this your definition of life: anything but "a bunch of humans performing roles that model the mechanisms of life".

I thought you were defending the view that it all depended on the definition... Based on what you complain in this thread without stating your own take on the issue, this example is a perfect satirical example of "life"...

 

[sokrates]

DaveC, what's your definition of life? This is very long thread, so if you stated it already, it's worth repeating.

Mine had been: A self replicating, adaptable system.

This leaves out crystals, and includes viruses. I'd want to have prions in the ambiguous middle, but it excludes them entirely.

Well put. I agree with this. I am just curious though, what are the adaptation mechanisms of a virus?

 

[Phrak]

Well put. I agree with this. I am just curious though, what are the adaptation mechanisms of a virus?

Can't say as I know much about viruses, or biology for that matter. Mutation and genetic mixing between subspecies comes to mind.

 

[CRGreathouse]

but self replication is quite dangerous that would leave all strile organisms out of the definition so many crops would count as life anymore so many sterile organisms etc tehy can only grow on their own thei can't replicate.

you could get around that at least a bit by saying you apply the definition only to cell sized entitys but still i would say excluding annything what can't grow anymore is a bit difficult

Fair enough. Do you have an alternate definition?

 

[DaveC426913]

After all those useless points (circular arguments, discussions on semantics, stating big remarks on how definitions narrow generalities), is this your definition of life: anything but "a bunch of humans performing roles that model the mechanisms of life".

I thought you were defending the view that it all depended on the definition... Based on what you complain in this thread without stating your own take on the issue, this example is a perfect satirical example of "life"...

You have not been following the discussion. You are interpreting my post in a vacuum.

Read https://www.physicsforums.com/showpost.php?p=2283100&postcount=77" (in particular, the last line) where CRG makes a satirical example of life based on kuzao's definition.

Then skip to https://www.physicsforums.com/showpost.php?p=2283234&postcount=80", where I demonstrate that CGR's satirical example is itself invalid, since it is so broad that anything could be defined that way.

 

[kuzao]

Fair enough. Do you have an alternate definition?

hmm

is still think that transcription and translation or the presence of rna and dna at the same time ist the most fitting definition. however i also think that this is a very strict biological /scientific definition.

the 'self replicating' defintion sounds a bit philosphical to me. if you applie it there is room for interpretation. if you are looking for this kind of defintion, i would include the ability to metabolzie.

there is something else. i think its a bit difficult to define life for single entitys. that would leave me with the need t use the word species. but i think the word species is not usefull because itself is a bit wobbly.

so how about: a group of similar organisms / entitys with the ability to metabloize and mechanism to ensure (or is promote a better choice?) the groups continued existence.

this would eliminate the problems of sterile organisms. because as long the group or species has some means of survival (be it growing, replication or something else) they would still fit in the definition. and the metabolizing part is limiting this to organic life and excluding viruses.

any thougs about this definition?

EDIT: argh some typos are ok but that was too much

 

[CRGreathouse]

You have not been following the discussion. You are interpreting my post in a vacuum.

Read https://www.physicsforums.com/showpost.php?p=2283100&postcount=77" (in particular, the last line) where CRG makes a satirical example of life based on kuzao's definition.

Then skip to https://www.physicsforums.com/showpost.php?p=2283234&postcount=80", where I demonstrate that CGR's satirical example is itself invalid, since it is so broad that anything could be defined that way.

I don't think your criticism in post #80 sticks; I don't think that most definitions would be tripped up by my (admittedly satirical) counterexample. But see post #83 where I was put back in my place by kuzao. :)

 

[CRGreathouse]

any thougs about this definition?

a group of similar organisms / entitys with the ability to metabloize and mechanism to ensure (or is promte a better choice?) the groups continued existence

I think it's an improvement over the more specific earlier one.

I do have some problems with it, though. What is "metabolize"? I think it's hard to define that without reference to life. (Feel free to disagree, with a definition!) Also, the more I think about it, the more difficulties I have with "similar". Not only is this abstract, but it also causes problems with symbiosis. What about humans and our symbiotic bacterial cultures? Worst, what about our mitochondria? How do we draw the line so those are includes but other symbiotes are not?