What gives DNA replicating ability?

[icakeov]

I am wondering about the actual preconditions that give rise to DNA replication.

Basically, what are the actual environmental conditions/factors that created the process of replication in the first place.

I gather before replication, there was random atom and molecule sorting, and at some point there was a recursive feedback loop that made certain formations keep happening and they responded well to specific atoms (the CHNOPS group)

So what exactly started the replication ability/process? recursive loop is just recursion, not necessarily replication?

Or is it recursion in combination with some other factor that gave rise to the ability to self-replicate? Or is it something different?

I haven't really found any clear answers or hypotheses on this online.

p.s. would it be possible to use snowflake to describe what it would need in order for its molecules to start making exact copies of themselves. After all, snowflakes, although different, all look predictably similar (a snowflake will never a formation that resembles a lightning bolt..)

 

[DaveC426913]

RNA was the precursor to DNA. And enzymes a precursor to RNA.

What makes DNA repliciable is that it spontaneously generates two half blueprints (the double part of the double helix). They can be unzipped into two fragments, and each fragment then automatically forms a counterpart, leading to two identical but independent copies of the same thing.

Snowflakes do not do this. They do not make copies of themselves, it is merely a starting process (independent of the snowflake i.e the moisture content, temperature, etc of the environment) that leads to similar end products. Snowflakes do not contain information for making copies of themselves, and they don't split to form more. Each snowflake is created, from scratch, in a vacuum of 'knowledge' of its predecessors.

 

[icakeov]

Thanks for your response Dave
So it is basically a random, spontaneous ability to make two copies of itself?
To put my question in another way, is there a specific property (or properties) that DNA has that if taken away, it wouldn't replicate itself, just like snowflake can't.
And vice versa, is there a property (or properties) that the snowflake misses which, if added, would make it replicate (not necessarily in the same way of course).

I am just wanting to grasp the concept of the "ability" to replicate and what gives rise to it.

 

[DaveC426913]

Thanks for your response Dave
So it is basically a random, spontaneous ability to make two copies of itself?

No. it is an evolved process that started with much simpler enzymes, then RNA (the details of this evolution are a bit murky to me).

There are similar processes in nature that are able to replicate themselves, the Citric Acid cycle is one, but it is way simpler than DNA replication. This is, unlike snowflakes, a true form of chemical duplication.

To put my question in another way, is there a specific property (or properties) that DNA has that if taken away, it wouldn't replicate itself, just like snowflake can't.

Going to have to leave this to those with a higher pay-grade than I.

And vice versa, is there a property (or properties) that the snowflake misses which, if added, would make it replicate (not necessarily in the same way of course).

Snowflakes being self-similar is only superficially like copying. There is nothing about the snowflake process that could result in replication.

Put another way: a snowflake can spontaneously be created in the complete absence of other snowflakes (and do, in each new snowstorm). They are nothing more than the ever-present physical properties of temperature and water molecules.

A strand of DNA can only be generated from another strand of DNA. It cannot spontaneously be created (without a billion preceding years of chemical evolution).Here's Wiki's take:
https://en.wikipedia.org/wiki/DNA_replication
Don;t worry too much about big words, just get the idea of how it actually is able to split and then make a two new copies of itself.

 

[rootone]

Each base in one of two helixes necessarily requires a specific complementary base in the other helix.
So thus one helix encodes the blueprint for reconstructing the other helix = replication.
The actual process by which one half of DNA reproduces the other half is complicated and involves RNA in different forms and some special proteins.
That is not theoretical, it's observed.

 

[icakeov]

Thanks for all your thoughts.
Dave, I had no idea there was another replicator like DNA, such as Citric Acid. So can citric acid "maintain" itself and build further "structures"?

And as for the snowflake, I guess, those atoms took a different turn with their bonding. Just not a replicating one. Instead, just building designed structures that would last only for that lifetime.

And basically it was all a gradual process of certain enzymes starting to replicate themselves that then built into RNA and finally DNA. And the observed process above is how it works.

 

[DaveC426913]

So can citric acid "maintain" itself and build further "structures"?

No. It's too simple. But give it a half billion years...

And as for the snowflake, I guess, those atoms took a different turn with their bonding. Just not a replicating one. Instead, just building designed structures that would last only for that lifetime.

Snowflakes will never replicate. They are composed of H₂O only. They cannot form more complex molecules the way carbon can.

 

[Hornbein]

I am wondering about the actual preconditions that give rise to DNA replication.

Basically, what are the actual environmental conditions/factors that created the process of replication in the first place.

I gather before replication, there was random atom and molecule sorting, and at some point there was a recursive feedback loop that made certain formations keep happening and they responded well to specific atoms (the CHNOPS group)

So what exactly started the replication ability/process? recursive loop is just recursion, not necessarily replication?

Or is it recursion in combination with some other factor that gave rise to the ability to self-replicate? Or is it something different?

I haven't really found any clear answers or hypotheses on this online.

p.s. would it be possible to use snowflake to describe what it would need in order for its molecules to start making exact copies of themselves. After all, snowflakes, although different, all look predictably similar (a snowflake will never a formation that resembles a lightning bolt..)

DNA doesn't really have replicating ability. DNA all by itself will not replicate. It is part of a complicated system that replicates DNA. You CAN say that DNA is easier to replicate than are the vast majority of molecules.

RNA might occasionally self-replicate spontaneously. It would form a complementary strand then maybe a higher temperature or something like that would shake that strand off. Repeat, and you've replicated the original strand. I think you would be better off asking your question about RNA.

You might also look at prions, which are sort of like viruses but have nothing to do with RNA.

 

[DaveC426913]

DNA doesn't really have replicating ability. DNA all by itself will not replicate. It is part of a complicated system that replicates DNA.

Yeah. Same with the Citric Acid cycle.

I thought that the nitty-gritty details of the process of replication would be too much. (They're certainly too much for me.)

 

[icakeov]

So basically these structures have replicating capacity but cannot replicate unless they have an external environmental process that will make them replicate?

I am guessing this might be a protective cell membrane that performs specific functions that allow DNA to replicate? No cell walls, no replication...

And could it be that these DNA (or RNA, and simple enzyme molecules before that) just combined and combined until they were in an environment where another independent stimulus was able to make copies of them?

 

[Hornbein]

So basically these structures have replicating capacity but cannot replicate unless they have an external environmental process that will make them replicate?

I am guessing this might be a protective cell membrane that performs specific functions that allow DNA to replicate? No cell walls, no replication...

And could it be that these DNA (or RNA, and simple enzyme molecules before that) just combined and combined until they were in an environment where another independent stimulus was able to make copies of them?

Yes. They aren't really self-replicating. Take out any part of the system and the whole thing falls fails. It is a mystery how this came about. But there is no reason to think the mystery is unsolvable.

 

[DaveC426913]

I am guessing this might be a protective cell membrane that performs specific functions that allow DNA to replicate? No cell walls, no replication...

Yes. It is thought that the cell (basically a collection of hydrophobic, lipophilic molecules) was the precursor to replication. Hydrophobic means they repel water. Lipophilic means they are attracted to their own fatty oily, selves. The combination of these two results in the spontaneous creation of enclosed spaces - much like a bubble can form in soapy water.

The cell allows concentrations of useful molecules to build up, creating a soup from which more complex reactions can occur without being imediately torn apart by every passing lap of a wave in the ocean, or every ionized molecule that comes along and wants to latch on.

 

[Ygggdrasil]

I am wondering about the actual preconditions that give rise to DNA replication.

Basically, what are the actual environmental conditions/factors that created the process of replication in the first place.

You're asking about a process called abiogenesis, how living, self-replicating biological systems emerged from non-living chemical precursors. The exact mechanisms of abiogenesis are not well understood and an active area of research. Here is a good article in Scientific American from Jack Szostak, one of the leading researchers in the field, some of our current thoughts on abiogenesis: https://www.mcb.ucdavis.edu/faculty-labs/scholey/journal%20papers/ricardo-szostak-sa2009.pdf

For more links and discussion, see my previous post on this previous PF topic: https://www.physicsforums.com/threads/a-question-about-natural-selection.743420/#post-4690960

I'll quote the part that's most relevant to the discussion about whether DNA is a special molecule for its replicating ability:
Life is a property that comes about not from the molecules themselves, but from the interactions between the molecules – it is an emergent property of a collection of molecules. If you are mathematically inclined, here's one way to think about it. Consider a system of coupled non-linear differential equations. These differential equations might describe different interactions between molecules in a living system. Now, depending on the parameters of that set of differential equations, the system will behave differently. For some sets of parameters, the system will tend toward attractor points whereas for other parameters, the system will diverge away from repellor points. The system might enter a limit cycle and display oscillatory behavior for some parameter, while other parameters will lead to a chaotic system. These behaviors all depend on the initial values of the parameters of the system, the point in phase space at which these systems begin. Life, in this somewhat simplified view, is the region of phase space that allows the system to exist as a self-replicating system that can extract energy and building blocks from its surroundings. All you need to do is to find the right collection of molecules (i.e. the right set of differential equations) and set them up at the correct point in phase space, and you can create a living system.

 

[icakeov]

That's it! Thanks Ygggdrasil! That makes a lot of sense, I love the math equation analogy! Let me process this one for a bit more and get back if anything becomes further unclear. :)