Comment by erichocean | Hacker News Reader

Comment by erichocean | Hacker News Reader

Parent Full thread

This is what I mean by random: no DNA sequence is privileged over any other, and no (known) physical process produces anything but random DNA sequences (excluding, of course, copying already useful DNA sequences).

DNA has about as much structure as bits on a disk (with coding for one of 20 amino acids as the "bits"). No DNA sequence is more likely than any other to exist.

I think that means we need to identify strong physical processes that produce useful DNA strands; you, apparently, aren't as concerned about it. Maybe you're right, but from where I'm sitting, it's hard to imagine what those physical processes might be since the strands they must produce are extremely, unimaginably rare in practice.

DNA is basically information[0], and we literally have no example of a chemical process producing valid DNA information, nor is it all obvious how such a process might work in practice. In the past, large amounts of time + equal likelihood of producing random DNA was considered sufficient to think "well, useful DNA stands could appear randomly." We now know that's extremely unlikely to the point of being effectively impossible, statistically-speaking.

[0] https://www.nature.com/scitable/topicpage/dna-is-a-structure...

But some DNA sequences are privileged over others!

The mechanisms for producing new DNA sequences involves copying existing DNA sequences. Thus, the ones that exist are privileged over the ones that do not exist (yet), and the adjacent sequences are privileged over a random sequence.

> No DNA sequence is more likely than any other to exist.

It is far more likely for a DNA sequence very similar to my own to exist than a random sequence.

> we need to identify strong physical processes that produce useful DNA strands

We have already identified those processes! We know quite well how the machinery of DNA replication works.

If we care about the first DNA molecule to ever exist it's a very different question. We don't need to find a physical process that produces a modern DNA molecule from 'raw parts', rather one that takes not-quite-DNA and converts it into DNA.

> it's hard to imagine what those physical processes might be since the strands they must produce are extremely, unimaginably rare in practice.

Can you imagine slightly simpler DNA? Say just a bit shorter? What's the simplest molecule we might still call DNA, that is reproducing? Can we imagine machinery that would produce that?

I think it's very reasonable to think such machinery could exist, even if we don't know the exact mechanisms involved. We know that RNA can self-reproduce, and also produce proteins, so it's reasonable to think that machinery to produce RNA strands could evolve to produce DNA strands (for example).

The only involvement randomness has in this whole process are (relatively) rare and infrequent changes to self-replicating molecules, and (potentially) the initial formation of a self-replicating molecule.

It is irrelevant how many possible DNA sequences there are, or how much information is stored within them, as we know new sequences are derived from previous ones.

> If we care about the first DNA molecule to ever exist it's a very different question. We don't need to find a physical process that produces a modern DNA molecule from 'raw parts', rather one that takes not-quite-DNA and converts it into DNA.

We haven't found that, and apparently aren't even close. We don't even have any idea what something like that might look like, or even more critically: given all the incredibly, insanely, unbelievably rare DNA sequences that exist in the world today, why is such a fundamental process capable of producing them not abundant as fuck already? Where'd it go? Why is this process even a mystery in 2020? It should be ubiquitous; in fact, all of the primordial soup mechanisms should be. Certainly that's what we expected when the theory was developed, and it hasn't panned out.

Anyway, I think we've exhausted this topic. Thanks for commenting.

> We haven't found that, and apparently aren't even close.

We do have ideas! Specifically, within the RNA world hypothesis, the transition period is called the virus world [0]

> given all the incredibly, insanely, unbelievably rare DNA sequences that exist in the world today,

We have a good understanding of where diversity comes from, I'm not sure what point you're making here.

> why is such a fundamental process not abundant as fuck already. Where'd it go? Why is this even a mystery?

I don't think anyone thinks this process need be 'fundemental', though it definitely is pivotal. It only really needed to happen once, and then DNA was off reproducing and spreading by itself. That said, it looks like viruses converting RNA to DNA could still be happening today.

In general, we don't expect novel self-reproducing molecules to arise today, because they are out-competed by existing self-replicating molecules. In a world where nothing is replicating the first replicator is king. In today's world a brand new replicator is food for something else.

> Maybe it's possible that your romantic view of how this all happens (pseudo-Darwinian circa 2020) isn't telling the whole story?

I don't think I, or anyone else really, is claiming to tell the whole story - just that we have good reason to believe this came about through physical processes, and no evidence to believe... well I'm not sure what else there could be.

What are you proposing?

[0] https://en.wikipedia.org/wiki/RNA_world#Evolution_of_DNA

Interesting discussion. I’d like to ask a sincere question:

Wouldn’t a system A that is capable of encoding another complex system B, need to be as complex in order to encode all the information in the result?

It’s like a compression algorithm, you can encode the information, but the complexity level of that information is still there (also the difficulty in compressing the information increases very fast - exponentially or maybe even factorially).

So if the most basic protein sequence requires so many bits of information, wouldn’t anything capable of producing that (in a non-random manner) also require at least that level of information (if not more).

It doesn’t matter what process we call systems A and B.

So it seems if randomness doesn’t solve the problem (because math), then the only conclusion is that there is a fundamental requirement for intentionality.

It's possible for a simple thing to encode something more complex, deterministically.

The prime example is The Game of Life - simple rules from which complex behaviour emerges.

This idea of information is one we're putting onto the system, not some inherent attribute. Yes, the encoding of a protein needs to have enough information to produce that protein (or a family of proteins), but that says nothing about the process that created the encoding.

For example, a strand of RNA can be spliced in many different ways to create many different proteins [0] and this process can go weird in many ways. New sequences will arise from this process, even though they weren't 'intended' to.

[0] https://en.wikipedia.org/wiki/RNA_splicing

Yes, and useful proteins are basically the equivalent of "oscillators" or "spaceships" in the game of life. But must runs of the game of life are not oscillators or spaceships, just like most proteins are useless.

That's why the "initial condition" is so important, and why DNA is so important: without a good "start state", you get useless results—just like in the game of life.

What we are trying to find is not Conway's rules for the game of life, but this: how do we produce useful starting states (DNA) with a physical system? And more importantly, how do we create those starting states preferentially (i.e. non-randomly)?

We still need a model for how useful DNA (which corresponds to the "initial state" in the game of life) gets created. And we have no model for that right now, other than assuming unique random initial states are continually occurring and letting the law of large numbers eventually "find" winners.

Minor side note, but most runs of the game of life actually will produce spaceships and/or oscillators, even starting from a random configuration. (Initialize a 100 x 100 box of cells randomly, and you're virtually guaranteed to get several gliders flying off of the resulting mess.)

For DNA, at least, it could have come from RNA (as per the link in my last post).

While I don't think the pre-biotic problem is solved at all, we have a lot more models of how it could have happened than you seem to credit - this is after all a huge research area.

For example, here is one [0], and here is a whole journal issue on the subject [1].

I found these by searching for 'evolution of DNA' and 'evolution of RNA'.

Now, these models all include some randomness, but in no way does anyone assume "unique random initial states are continually occurring... letting the law of large numbers eventually "find" winners"

The models show plausible environments where pre-biotic synthesis of RNA (or RNA pre-cursors) can occur, and stabilise.

This model you keep bringing up - randomly selecting a molecule from all possible combinations of atoms and saying 'enough time will get you one that works' - is not mentioned anywhere that I have seen. Perhaps some lay-people (of which I am definitely one!) believe it, but as you point out it is so obviously implausible it falls down on first inspection.

There are other models (lots of them!) and they don't rely on this pure randomness.

[0] https://phys.org/news/2018-01-chemical-evolution-dna-rna-ear...

[1] https://www.mdpi.com/journal/life/special_issues/evolution-R...

The Game of Life doesn't produce complex behavior from simple rules.

The complex behavior comes from a large enough random starting state combined with a very low minimal required complexity to see something interesting. Also, even for a short interesting run of local behavior, the game never produces a stable behavior that grows in complexity beyond the initial information encoded in the random state. (i.e. if there is a bubble of cool stuff happening somewhere on the 2d plane, something usually interferes with it and destroys that pattern - like waves in the ocean, even when the energy curves combine to form a wave once in a while, they are limited and temporary).

So the Game of Life is actually an example that the system is limited to the information encoded in the initial starting state.

In the starting state there is either:

- a large enough random search space (i.e. a million random attempts with a 100x100 board might get something cool looking)

- intentionality (a person can design a starting state that can produce any possible stable system)

Reply on news.ycombinator.com