Replicating molecule..

[kevin1981]

What is the difference between a normal molecule and a replicating molecule like RNA or DNA ?

What mechanism triggers a non replicating molecule to suddenly start replicating itself ?

Also, when RNA starting replicating, did it already have the instructions to build a cell around itself to keep it safe or was it floating around on its own without any protection ?




Just musing really, but cheers for any answers

[Selfsim]

What is the difference between a normal molecule and a replicating molecule like RNA or DNA ?

In organic chemistry, molecular size and complexity.
Very large and complex molecules such as RNA/DNA are self-replicators.

What mechanism triggers a non replicating molecule to suddenly start replicating itself ?

Autocatalysis is hypothesized as possibly being a possible phase in the lead-up to organic molecular self replication:

A single chemical reaction is said to be autocatalytic if one of the reaction products is also a catalyst for the same or a coupled reaction.[1] Such a reaction is called an autocatalytic reaction.

So-called 'clock reactions' such as the Belousov–Zhabotinsky reaction are one such example of autocatalysis. (Others are also known as existing).

Also, when RNA starting replicating, did it already have the instructions to build a cell around itself to keep it safe or was it floating around on its own without any protection ?

The evolution of cell membranes is the subject of yet other hypotheses. In general lipid formation has been demonstrated (in lab environments) as leading towards fundamental membrane-like functionality.

[DaveC426913]

There are much simpler replicators.
They're not really useful as a base for transcription, since they're super simple.
It's not a self-replicating molecule, it's a cycle of molecules whose outcome is a second copy of the first molecule.

I wish I could remember what it's called.

It's got something to do with Chlorine and occurs near hydrothermal vents, where the right elements are available.

[Selfsim]

There are much simpler replicators.
They're not really useful as a base for transcription, since they're super simple.
It's not a self-replicating molecule, it's a cycle of molecules whose outcome is a second copy of the first molecule.

In the context of discussions about modern biological mechanisms and processes, 'self-replication' is fairly well explained.

In the context of so-called 'pre-biotic' chemistries however, I think the terms 'replication' and more specifically, 'self-replication', really take on a different meaning.

I wish I could remember what it's called.

It's got something to do with Chlorine and occurs near hydrothermal vents, where the right elements are available.

I'd be interested to see references/papers on this(?)

[Jens]

What is the difference between a normal molecule and a replicating molecule like RNA or DNA ?

I'm not exactly sure what you mean by a "replicating molecule." A molecule that is created by some program? In that case, I think that all proteins are replicating molecules. Or do you mean one that has a code in it that is used to make other molecules?

[DaveC426913]

I'm not exactly sure what you mean by a "replicating molecule." A molecule that is created by some program? In that case, I think that all proteins are replicating molecules. Or do you mean one that has a code in it that is used to make other molecules?

He mentioned RNA and DNA. Surely he literally means self-replicating.

[Jens]

He mentioned RNA and DNA. Surely he literally means self-replicating.

But they're not self-replicating as far as I know. A molecule of RNA or DNA left in a solution will not replicate.

[Cougar]

In organic chemistry, molecular size and complexity.....
Autocatalysis is hypothesized as possibly being a possible phase in the lead-up to organic molecular self replication....

Yes, and a good introduction to something like 20 years of study on the question is At Home in the Universe by Stuart Kauffman.

[Selfsim]

But they're not self-replicating as far as I know. A molecule of RNA or DNA left in a solution will not replicate.

The so-called 'translational apparatus', (ribosomes and other proteins), are themselves derived from subunits of the RNA molecule (rRNA).
In this sense, RNA is still referred to as self-replicating (tis 'the origin').

How functional ribsosomes came about in the first place, is one of the big questions, though.
They have been artificially synthesised (by Ventner etc) but this was done based on the known structures of modern fully functional ribosomes.

[Selfsim]

Yes, and a good introduction to something like 20 years of study on the question is At Home in the Universe by Stuart Kauffman.

Yep .. even though he cast a big opinion in his conclusions about the 'inevitability' of it all.

[Selfsim]

The so-called 'translational apparatus', (ribosomes and other proteins), are themselves derived from subunits of the RNA molecule (rRNA).
In this sense, RNA is still referred to as self-replicating (tis 'the origin').

How functional ribsosomes came about in the first place, is one of the big questions, though.
They have been artificially synthesised (by Ventner etc) but this was done based on the known structures of modern fully functional ribosomes.

Interestingly, it seems that researchers have only just recently succceded in engineering a ribosome to replicate itself for the very first time:

Normally when copying RNA, an enzyme would add single bases (C, G, A or U) one at a time, but the new ribozyme uses three bases joined together, as a 'triplet' (e.g. GAU). These triplet building blocks enable the ribozyme to copy folded RNA, because the triplets bind to the RNA much more strongly and cause it to unravel—so the new ribozyme can copy its own folded RNA strands.

Previously, they've only been able to get ribosomes to replicate straight strands of RNA, thus blocking its ability to copy its (very) folded self.

Also interesting, (from the same article), is that triplet binding seems to also be a 'sweet spot' for opening up the folds, whilst maintaining a high replication accuracy.

[DaveC426913]

But they're not self-replicating as far as I know. A molecule of RNA or DNA left in a solution will not replicate.

I would argue they are self-replicating in that they are able to replicate themselves.

What you're describing sounds to me more like spontaneous replication. i.e. that they would replicate if simply left to their own devices. They won't of course, but I don't think that's what the OP is looking for anyway.

[Jens]

I would argue they are self-replicating in that they are able to replicate themselves.

I know it’s a subtle point, but I was thinking that it is the cell that is self-replicating, and that the genome provides the code that guides the process.


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[DaveC426913]

In the context of discussions about modern biological mechanisms and processes, 'self-replication' is fairly well explained.

In the context of so-called 'pre-biotic' chemistries however, I think the terms 'replication' and more specifically, 'self-replication', really take on a different meaning.

I'd be interested to see references/papers on this(?)

Ah! Found it again! Not chlorine - citric acid!!

https://en.wikipedia.org/wiki/Citric_acid_cycle

It's a cyclic reaction that, provided the right elements, produces more citric acid, which can then be used to start another cycle.

Again, it's too simple a molecule to encode anything useful, but it's a start. Give it a billion years or so...

[Selfsim]

There are other so-called 'self-replicators' also.

It has been demonstrated that amyloid structures (in a 'soup') can spontaneously form from simple amino acids which settle at just the right sites, and then chemically combine with eachother. Amyloids are composed of short peptides and form fibres which are also able to accelerate chemical reactions (same as enzymes). This peptide synthesis mechanism, when applied to the amyloids themselves, gives rise to the 'self-replication' argument.

The researchers campaigning for this one, argue that the formation and replication mechanism is more 'plausible' (to them) than the 'RNA-first' hypothesis of abiogenesis.

Paper here.

[Selfsim]

Ah! Found it again! Not chlorine - citric acid!!

https://en.wikipedia.org/wiki/Citric_acid_cycle

It's a cyclic reaction that, provided the right elements, produces more citric acid, which can then be used to start another cycle.

Again, it's too simple a molecule to encode anything useful, but it's a start. Give it a billion years or so...

Yep .. thanks.
A key part of metabolism .. which makes available the energy for cellular processes, (including self-replication).

[kevin1981]

Thanks for all the comments, i have just re-read the thread and i enjoyed reading what everyone had to say..

It seems given the right conditions, life can get going rather quickly, well maybe taking 500 million years or so..

Would it be fair to say that in the future, say 100/200 years from now, Humans would have a fairly good idea of most, it not all pathways that led up to non-organic chemistry evolving into organic chemistry.. ?

One would think that the earlier we look back, the simpler, less complex the chemistry would be. But it seems to be a hard task to work out how "simple" non-organic chemistry transitioned into the first biochemicals..

[Selfsim]

.. It seems given the right conditions, life can get going rather quickly, well maybe taking 500 million years or so..

I think some care also needs to be taken in making such assertions because 'the right conditions' is still an hypothesis under test, with only terrestrially sourced evidence from its past, supporting it. With further evidence (from beyond Earth), it may also turn out that what we think are 'the right conditions' is also capable of producing no life over a similar period. (Mars, for instance, may turn out to be an example).

Put simply, our view of what it takes, is incomplete until data from beyond Earth better constrains 'the right conditions'.

Would it be fair to say that in the future, say 100/200 years from now, Humans would have a fairly good idea of most, it not all pathways that led up to non-organic chemistry evolving into organic chemistry.. ?

Our definition of what is, and what isn't, 'organic chemistry' is relevant here. Wiki says (my emboldenments):

In chemistry, an organic compound is generally any chemical compound that contains carbon. Due to carbon's ability to catenate (form chains with other carbon atoms), millions of organic compounds are known. Study of the properties and synthesis of organic compounds is the discipline known as organic chemistry. For historical reasons, a few classes of carbon-containing compounds (e.g., carbonates and cyanides), along with a handful of other exceptions (e.g., carbon dioxide), are not classified as organic compounds and are considered inorganic. No consensus exists among chemists on precisely which carbon-containing compounds are excluded, making the definition of an organic compound elusive. Although organic compounds only make up a small percentage of the Earth's crust, they are of central importance because all known life is based on organic compounds.

Notice how this definition (and consensus) implies 'life' when used in a terrestrial context .. (because 'life' is only known to exist on Earth). It also references 'historical reasons' for the distinction of organic/inorganic. These 'historicial reasons' clearly currently pertain only to Earth, Earth's life and human's known histories. The implications of this is that 'organic/inorganic' may not necessarily be as clear where organic compounds, (for eg), are found beyond Earth, in a lifeless environment.

The point here (IMO), is that thinking that inorganic chemistry always necessarily evolves into life's specific organic chemistry under 'the right conditions', (ie: Earth's), is only evidenced, (thus far), in the Earth only context, which whilst reasonable, is still unsupported in a non-Earth environment.

Astrobiologists, use a similar definition:

Organic: molecules that contain carbon atoms. The distinction from “inorganic” is historically arbitrary; some carbon-containing molecules such as carbides, or simple carbon-oxygen combinations (like CO2), are considered inorganic.

Perhaps your use of your term 'non-organic' rather than 'inorganic' was intended to denote the same as the points I'm making above(?)

One would think that the earlier we look back, the simpler, less complex the chemistry would be. But it seems to be a hard task to work out how "simple" non-organic chemistry transitioned into the first biochemicals..

Abiogenesis is an hypothesis-under-test. Lab-testing and bio-synthesis are parts of that.
Earth's geological processes wiped out most historical records which may have supported various parts of the Abiogeneses hypothesis pertaining to Earth's transitional phasing towards life.

Exploration of environments beyond Earth is another part of Abiogenesis research also.
We don't know the outcomes of the latter testing yet, and that's what also contributes to making it 'hard' (your usage of the term here).

[kevin1981]

I think some care also needs to be taken in making such assertions because 'the right conditions' is still an hypothesis under test, with only terrestrially sourced evidence from its past, supporting it. With further evidence (from beyond Earth), it may also turn out that what we think are 'the right conditions' is also capable of producing no life over a similar period. (Mars, for instance, may turn out to be an example).

Put simply, our view of what it takes, is incomplete until data from beyond Earth better constrains 'the right conditions'.

Oh yes, of course, that is a great point to make, i didn't really think through what i was saying..

Totally makes sense that just because life got going hear on Earth, it does not necessarily mean it will anywhere else..

Perhaps your use of your term 'non-organic' rather than 'inorganic' was intended to denote the same as the points I'm making above(?)

I meant inorganic but i used the wrong term. I know very little about this subject but i have started reading a bit and i have been watching some lectures on youtube about how life may of arised on Earth.
I find it very interesting so i am trying to learn about it..

I thought it was a straight forward definition, inorganic material being what we describe as life, where organic material is non-life. But i guess what you are pointing to is that it is not
as straight forward as that..

In chemistry, an organic compound is generally any chemical compound that contains carbon. Due to carbon's ability to catenate (form chains with other carbon atoms), millions of organic compounds are known. Study of the properties and synthesis of organic compounds is the discipline known as organic chemistry. For historical reasons, a few classes of carbon-containing compounds (e.g., carbonates and cyanides), along with a handful of other exceptions (e.g., carbon dioxide), are not classified as organic compounds and are considered inorganic. No consensus exists among chemists on precisely which carbon-containing compounds are excluded, making the definition of an organic compound elusive. Although organic compounds only make up a small percentage of the Earth's crust, they are of central importance because all known life is based on organic compounds.

I see, this makes sense. Basically we call all carbon based materials organic because all life uses carbon but the definition is not strictly true as some carbon based materials are not classified as life..

The point here (IMO), is that thinking that inorganic chemistry always necessarily evolves into life's specific organic chemistry under 'the right conditions', (ie: Earth's), is only evidenced, (thus far), in the Earth only context, which whilst reasonable, is still unsupported in a non-Earth environment.

What do you mean by, “is still unsupported in a non-Earth environment” ?

Thanks as always.

[kevin1981]

I thought it was a straight forward definition, inorganic material being what we describe as life, where organic material is non-life. But i guess what you are pointing to is that it is not as straight forward as that.

Correcting my mistake here, i got the terms the wrong way round !

I thought it was a straight forward definition, organic material being what we describe as life, where inorganic material is non-life. But i guess what you are pointing to is that it is not
as straight forward as that

[Selfsim]

Correcting my mistake here, i got the terms the wrong way round !

No worries .. just as further clarification, (should anyone accuse me of plagiarising others' words), the quote defining organic/inorganic was verbatim from Wiki (organic compound .. link here).

I thought it was a straight forward definition, organic material being what we describe as life, where inorganic material is non-life. But i guess what you are pointing to is that it is not as straight forward as that.

Actually, the term 'organic material' is usually closer to meaning material that has been processed specifically by living things, than 'organic compound' is.

However, (as I think you mean), whenever we see the headlines of say, "Organic compounds detected on Mars", (or elsewhere in reference to anywhere beyond planet Earth), it will help to remember this conversation and that an organic compound is a long, complex and as yet unknown number of steps away from truly implying the presence of 'life'​.

[Selfsim]

The point here (IMO), is that thinking that inorganic chemistry always necessarily evolves into life's specific organic chemistry under 'the right conditions', (ie: Earth's), is only evidenced, (thus far), in the Earth only context, which whilst reasonable, is still unsupported in a non-Earth environment.

What do you mean by, “is still unsupported in a non-Earth environment” ?

Put more simply, we have never found any objective evidence of life on other habitable moons or planets, even though we know some of them do have beyond simple organic compounds.

Based on this, we cannot say we have objective evidence that organic compounds found in habitable environments, (aka: 'the right conditions'), beyond Earth's, always evolve into life.

Usually, in order to preserve the 'exo-life exists' argument in this circumstance, proponents of it will then argue that 'the right conditions' may have existed in that planet's/object's past and we just haven't explored it enough to find that it may have once had life, or it presently may have difficult-to-find life (perhaps sub-surface microscopic bacterial life). However notice the 'may' word. In this case, 'may' implies what the proponent believes as being 'a possibility' and their counter-argument attempts to counter a scientific, factually accurate, objective statement with only their belief (or opinion) - which is hardly an apples-to-apples counter-argument. This counter is then put forward as evidence that inorganic compounds will therefore 'evolve' into life's organic compounds under 'the right conditions', even though there is no evidence for this, other than the reasonable evidence from Earth's geological and biological evolutionary records. The usual conclusion formed then is: that planet/moon just didn't experience 'the right conditions', thus sustaining the initial hidden assumption/belief that life exists/existed there.

The point is that in the various hypothesised abiogenesis models, there are clear phases and distinct steps thought to be necessary 'precursor stages' in the hypothesised lead-up to a self-replicating, evolvable molecule. None of these proposed hypothetical steps have been met with objective examples in a natural environment beyond Earth's already alive biosphere. Abiogenesis is a good working hypothesis for investigation purposes, however .. and it is presently 'under test' with Solar System exploration (as is Evolution).

[kevin1981]

However, (as I think you mean), whenever we see the headlines of say, "Organic compounds detected on Mars", (or elsewhere in reference to anywhere beyond planet Earth), it will help to remember this conversation and that an organic compound is a long, complex and as yet unknown number of steps away from truly implying the presence of 'life'​.[/QUOTE]

Yes i definitely will, it make sense what you are saying ! I will also remember that organic material is usually something produced by life to be used by life. So if i was discussing something like what my carpet was made out of, i would say inorganic compounds made up of molecules..

[COLOR=#333333]Put more simply, we have never found any objective evidence of life on other habitable moons or planets, even though we know some of them do have beyond simple organic compounds.

Based on this, we cannot say we have objective evidence that organic compounds found in habitable environments, (aka: 'the right conditions'), beyond Earth's, always evolve into life.

Usually, in order to preserve the 'exo-life exists' argument in this circumstance, proponents of it will then argue that 'the right conditions' may have existed in that planet's/object's past and we just haven't explored it enough to find that it may have once had life, or it presently may have difficult-to-find life (perhaps sub-surface microscopic bacterial life). However notice the 'may' word. In this case, 'may' implies what the proponent believes as being 'a possibility' and their counter-argument attempts to counter a scientific, factually accurate, objective statement with only their belief (or opinion) - which is hardly an apples-to-apples counter-argument. This counter is then put forward as evidence that inorganic compounds will therefore 'evolve' into life's organic compounds under 'the right conditions', even though there is no evidence for this, other than the reasonable evidence from Earth's geological and biological evolutionary records. The usual conclusion formed then is: that planet/moon just didn't experience 'the right conditions', thus sustaining the initial hidden assumption/belief that life exists/existed there.

What would satisfy you as to what would be good evidence found on another planet.. For example, say we go to mars, what would be needed to be able to say, yes, life did get going there..

[COLOR=#333333]The point is that in the various hypothesised abiogenesis models, there are clear phases and distinct steps thought to be necessary 'precursor stages' in the hypothesised lead-up to a self-replicating, evolvable molecule. None of these proposed hypothetical steps have been met with objective examples in a natural environment beyond Earth's already alive biosphere. Abiogenesis is a good working hypothesis for investigation purposes, however .. and it is presently 'under test' with Solar System exploration (as is Evolution).

I have watched some youtube videos and i read an article yesterday and it was talking about possible hypothesises as to how life may of got going. First there may of been some sort of RNA world or even maybe a precursor to RNA. Then it explained maybe a primitive proto-cell was first and then they suggested metabolism was the first process that got going..

It it very interesting stuff and i am going to watch a few more youtube videos about it..

It does seem as the process from inorganic compounds to biological life is a complex one and i get the feeling that they are a little stumped as to what the steps are to go from one to the other..

But i realise we are in our infancy in this on going discovery and a lot needs to be learnt, but that does not mean that it will not be learnt, it is just that, nobody knows you long this process could take..

[Shaula]

Yes i definitely will, it make sense what you are saying ! I will also remember that organic material is usually something produced by life to be used by life. So if i was discussing something like what my carpet was made out of, i would say inorganic compounds made up of molecules..

Bad news - a chemist would probably disagree unless you have metal carpets.

https://en.wikipedia.org/wiki/Organic_compound

[kevin1981]

Bad news - a chemist would probably disagree unless you have metal carpets.

https://en.wikipedia.org/wiki/Organic_compound

Ahh i see !

I think i am thinking that all life uses carbon based chemistry so it is organic. But i guess there can be non-life substances that also use carbon based chemistry that could be considered as organic. This is what Selfsim pointed out to me earlier.

[Selfsim]

Bad news - a chemist would probably disagree unless you have metal carpets.

https://en.wikipedia.org/wiki/Organic_compound

Yes .. I think the the point you might be making here (?) is that we can't really make any golden rules (or strict definitions) when it comes to what is/isn't an 'organic' compound(?)
From the Wiki page (my underlines):

As described in detail below, any definition of organic compound that uses simple, broadly applicable criteria turns out to be unsatisfactory, to varying degrees. The modern, commonly accepted definition of organic compound essentially amounts to any carbon containing compound, excluding several classes of substances traditionally considered as 'inorganic'. However, the list of substances so excluded varies from author to author. Still, it is generally agreed upon that there are (at least) a few carbon containing compounds that should not be considered organic. For instance, almost all authorities would require the exclusion of alloys that contain carbon, including steel (which contains cementite, Fe₃C), as well as other metal and semimetal carbides ...

However, the phrase 'organic material', (at least in Astrobiology circles), tends to lean more towards 'life' than 'organic compound'(?) Mind you, this is still admittedly contentious and seems to vary depending on the context.

Personally speaking, I really don't 'warm' too much, to discussions which critically depend only on the definitions of terms. The more interesting ones on this particular topic (at least for me) are the ones which go onto to distinguish the boundaries of where we can say whether, or not, some discovered compound is or isn't, a known by-product of life processes, (based on terrestrially sourced evidence).

[DaveC426913]

Carbon is not sufficient to make a compound organic. It is generally considered to need hydrogen as well.

CO2, CO, cyanide, diamond, carbonide, etc. are all carbon-based, but not considered organic.

OTOH, methane - simply a carbon atom surrounded by 4 hydrogens - is organic.

[Selfsim]

... OTOH, methane - simply a carbon atom surrounded by 4 hydrogens - is organic.

.. and thence Astrobiologists tend to get somewhat excited whenever methane is detected in some exo-atmosphere ..

[Selfsim]

Just rewinding the conversation a little back to this interesting comment by kevin (my underline):

... I think i am thinking that all life uses carbon based chemistry so it is organic.

The phrase 'life uses carbon based chemistry', (emphasis on 'uses'), also raises issues. An interesting point here (not kevin's though) is that there is no known way life could exist, if it wasn't based on the (self replicating) carbon chemistry we are familiar with (taken from terrestrially sourced evidence). And yet, in many Astrobiology conversations, 'life' becomes this 'thing' which can swap its base chemistry for some other variation of this base biochemistry. Its almost a (very) circular argument, given that there is absolutely no certainty that life's various highly complex biochemical pathways would function at all, if the known base chemistry was significantly different to what it is.

The point being exploited in such arguments, is that certain base pair sequences in our own genetic code contains variations .. However, Evolution driven by limited niche resources and selection, is science's explanation for this observation .. (and not anything drawn from any evidence which, I can see, which is part Abiogenesis hypotheses or bio-engineering?)

[Shaula]

Yes .. I think the the point you might be making here (?) is that we can't really make any golden rules (or strict definitions) when it comes to what is/isn't an 'organic' compound(?)

I'm not making any point, really. And certainly not arguing definitions for the sake of arguing definitions. Just a cautionary note to Kevin that might help when reading articles saying things like "Organic compounds found on planet X" - they are actually saying nothing about life. We find organic compounds on asteroids, in giant molecular clouds and so on. I think the terms for the definition he was using for organic is actually biogenic.