Where did DNA come from?

https://geneticsunzipped.com/transcripts/2021/8/26/where-did-dna-come-from

by andsoitis • 2 years ago

88 62 2 years ago

geneticsunzipped.com

panja• 2 years ago

There are some mysteries I don't think we'll be able to solve and that makes me sad

bregma• 2 years ago

It makes me glad. One's reach should always exceed one's grasp. Keep searching.

alas44• 2 years ago

“The mystery of life isn't a problem to solve, but a reality to experience.” Frank Herbert

exe34• 2 years ago

Feyman once spoke of how his arty friend thought that scientists miss out on the beauty of a flower when they try to understand its components. (To paraphrase, since I can't remember the exact words), He replied that a scientist can see the outer beauty of the flower as much as the poet - it's just that the scientist can see poetry on a larger scale (the ecosystem, the bees, the co-evolution) and smaller scale (the cellular biology, the biochemistry, the chemistry, the atoms themselves, and then further down into the subatomic particles, etc).

Just because you know how a car works doesn't mean that you can't enjoy a ride across the countryside.

indigochill• 2 years ago

If you take the view that existence is physics and physics is math, then doesn't this follow from Gödel's incompleteness theorems?

msla• 2 years ago

No, it doesn't, at least when applied to physics.

verisimi• 2 years ago

A: Watson and Crick

defrost2• 2 years ago

Photograph 51, by Rosalind Franklin (1952)

dekhn3• 2 years ago

Actually taken by Raymond Gosling, not Franklin.

Faaak2• 2 years ago

Sadly everyone forgets Rosalind Franklin, which played a huge part and even got the Nobel price after her death (she couldn't be recognized before, as she was... a woman).

coldtea• 2 years ago

That's the modern pop version. The reality is more mundane:

https://www.nature.com/articles/d41586-023-01313-5

https://www.nature.com/articles/nature01399

dekhn3• 2 years ago

Pretty much everything you said is wrong.

She didn't get the prize. She is well remembered (her paper is right after W&C in the 1953 Nature). Her gender was not why she was not recognized for the prize.

ggm• 2 years ago

Synergistic effects, catalytic effects and basic things like van der waals forces. Molecules in energy rich evironments which self assemble and become both antichaotic and self reproducing.

Why does water freeze in star patterns? Why are salt crystals regular shapes? It's energy efficient. They may be local minima in better packing choices but if some number of these arrive at the helical zipper, the rest is history.

Did mitochondria have any idea what they were doing agreeing to be engulfed? Was it a choice in a soup of competing mitochondria, to hide in a fat-bag and acquire skin?

It's a shit answer: it's a posh wordy version of "because".

Feynman said (better) that much physics is "we don't know" built on shakey foundations, that explanation is often invoking primitives we treat as axioms without knowing what makes them axiomatic. All subatomic explanations of particles ultimately go to "we don't know"

Biology is applied physics.

yamrzou• 2 years ago

Biology is applied physics.

Can Biology Be Reduced To Physics? — https://youtube.com/watch?v=A4yzK-8OGtc

genman2• 2 years ago

He claims that the way we study complex systems, like those in biology, simply can't be reduced to physics.

Then he goes on to claim that the first Newton law doesn't apply to biology: but when we look at the biological world, matter seems to move by itself all the time.

This is simply not true. If it was true then we could also claim that any chemical process (that is governed by physics) can't be reduced to physics. Which obviously we know to be not true.

metricspaces• 2 years ago

[emergence of order]

The Origins of Order: Self-Organization and Selection in Evolution (1991)

https://www.abebooks.com/9780195058116/Origins-Order-Self-Or...

Did mitochondria have any idea

It remains a possibility, not subject to fascile dismissal, that ‘our world’ is a side-effect of a self reflecting mind. You will note on serious reflection that all you know and experience is ‘image’ and ‘imagination’. Now that there is a ‘correspondence’ to an ‘outside reality’ is only obtained when there are 2 or more of ‘us sentients’ and we compare notes using ‘language’ (with all its limitations and to be understood in its maximal sense & associated limitations, including ‘expression’, ‘communication’ and ‘reading’).

Biology is applied physics

Not all applications of physical laws result in living forms. Physics can be applied to understand (some aspects) of biological entities given that they are (conceptuallyminimally in part) made of physical stuff subject to governing regime of matter we study as physics.

tetris112• 2 years ago

           DNA: file.c

    polymerase: gcc  (transcribes DNA→RNA)

           RNA: file.o file.m file
                (the last one is mRNA)

      ribosome: ./file  (translates mRNA→Protein)

       protein: (program in RAM)

     epigenome: (program in RAM changes file.c)

     RNA world: (different file.o's messing with
                 each other by some unknown program,
                 eventually giving rise to stable 
                 file.c files)

willis9362• 2 years ago

Has anyone written a simulator in this style? You'd want to sandbox it so it doesn't get flagged as a virus, but it might be fun.

tetris112• 2 years ago

In a sense, the historic development of GCC[1] is similar to this, relying on the previous version of GCC to compile the newer, whilst making modifications to the parser to allow the new symbols to parse.

1: "Trusting Trust" by Ken Thompson https://users.ece.cmu.edu/~ganger/712.fall02/papers/p761-tho...

fxj• 2 years ago

isnt it more like:

RNA: asm text file

Protein: compiled binary

also: t-RNA is a hybrid of RNA and amino acids, which is like a hash table

Faaak2• 2 years ago

AFAIK, it's even "worse" as ribosomes are made of RNA (rRNA). and amino acids are linked to small RNA (tRNA) in when translating the (coding) RNA.

RNA is the start of everything (see: RNA world)

acchow• 2 years ago

“Von Neumann Architecture”

getoffmycase2• 2 years ago

If I had a nickel for every terrible biology to computer processes analogy I saw on this website since joining, I’d probably have enough money to buy a beer. Which is what I feel I need after I see something like this.

Biology does not act like a computer. You cannot reduce biology to an operating system

TeMPOraL• 2 years ago

Biology does not act like a computer. You cannot reduce biology to an operating system

Nobody is doing that. Analogies are drawing rough outlines in the thought-space[0], they aren't a definition. As such, they are helpful.

[0] - Or latent space, if I want to make an analogy inside the analogy apologia.

Ralfp• 2 years ago

This is sometimes called „Andrew Grove Fallacy” after Intel Ceo’s interview in Newsweek where he famously commented how drug research should look at CPU engineering for inspiration to improve itself, missing point that in biology we dont have privilege of knowing how each part of the system works, compared to, eg. designing CPUs, and making invalid analogies.

jibal• 2 years ago

How does a computer act? I think your understanding of that is too narrow ... consult the Church-Turing thesis; biology computes. And an operating system is just one sort of program ... it makes no sense to talk about reducing to an operating system; that's a category mistake.

FrustratedMonky2• 2 years ago

Is there an alternative to analogies and metaphors when using language?

What terms/concepts should be used in their place?

dekhn3• 2 years ago

Parts of biology act like analog computers even if the whole of biology exceeds what we see in computing.

But more importantly: the existence of DNA demonstrates that information processing is universal and that there are many common aspects between current approaches to silicon-based information processing and biology-based information processing.

dang3• 2 years ago

Ok, but can you please make your substantive points informatively? Just putting someone else or the community down doesn't help. It just makes the thread shallow and dyspeptic.

If you know more than others do, that's great, but then please share some of what you know, so the rest of us can learn (edit: like you did here! https://news.ycombinator.com/item?id=36330052) If you don't want to do that, that's fine too, but in that case the thing to do is remind oneself that the internet is more or less wrong about everything and move on.

I know it's tempting to leave an empty negative comment to relieve oneself of annoyance, but this is the worst choice, at least on HN. It not only isn't the curious conversation we're looking for, it actively impedes it.

p.s. You're a good HN commenter generally - so thanks for that!

https://hn.algolia.com/?dateRange=all&page=0&prefix=true&sor...

UniverseHacker3• 2 years ago

This analogy is workable, but I would make some changes. For example, epigenetics don’t change file.c, but how readily the rest of the process interacts with it. The ribosome produces file, but isn’t the file itself, whereas in some of your other entries the bio part is analogous to the computer part.

theGnuMe3• 2 years ago

Nice, it's amazing how the analogy matches up so well.

UniverseHacker3• 2 years ago

I like that this article mentions the metabolism first hypothesis. It seems less popular, but much more plausible to me then “RNA world.” There are many natural situations where there is available chemical energy, and reactions very much like central carbon metabolism spontaneously occur. A gradual stepwise process from that to present day metabolism seems fairly straightforward if you also add in isolated units that can be selected for.

Importantly, and still relevant to modern day life is the fact that metabolic states contain information and themselves can be heritable.

pfdietz2• 2 years ago

For selection, you need something with "memory", like genes.

I've wondered if something like this could work: store information in templates formed in otherwise random organic solids. The idea would be that a molecule adsorbed onto a surface would be most stable if its shape and charge density matched the shape and charges of a hollow in the surface. These charged holes would be a kind of analog memory. They promote formation of the matching chemicals, since they'd make formation of them from precursors more energetically favorable. At the same time, the presence of the small molecules would encourage the formation of matching holes.

This mechanism should be testable in small scale systems, forming tars from a mixture of various monomers.

RNA/DNA would come later and take over from this primordial mechanism.

ambyra• 2 years ago

I like the "lipid world" hypothesis over the "RNA world". It reminds me of the chicken or the egg argument. I don't see how life could form outside of a controlled environment, like an egg or a seed. Something forms in a lipid that couldn't form in a harsh nature, the lipid pops, the something gets to hang out with the other somethings that formed in lipids nearby, and they get reabsorbed by lipids. Make sense to me. There are so many specific control mechanisms for getting inside of eggs, seeds, cells, etc. Seems like a fundamental part of life. I remember something from the "your inner fish" book, talking about how all of evolution in a body happens between layers.

UniverseHacker3• 2 years ago

Yes, as I understand it the metabolism first and lipid first ideas are related, in that you have some sort of micelle or vesicle that contains metabolism, and is partitioned off in a way that selection can act on them.

M95D• 2 years ago

But the paired RNA or DNA strands then bind together so tightly that they can’t separate without help from sophisticated enzymes, preventing them from making any new RNA or DNA.

No. They can be separated by temperature alone. See DNA denaturation phase during Polimerase Chain Reaction.

treyd• 2 years ago

This kind of thing is why I think cyclical changes of environmental conditions (temperature, light, etc) on short and long timescales was important for making the chemistry of early life work. There plausibly needs to be some way for enzymes and other processes to be switched on and off for various reasons, and if that just happened naturally through the day that would avoid the need for more sophisticated signalling/control machinery to have evolved spontaneously. It's easy to see how this could then evolve into the circadian rhythms that nearly all complex life on earth has as other processes were built into/around that basic behavior.

a_gnostic• 2 years ago

Midichlorians are the power house of thw cell.

utopcell• 2 years ago

Let me save folks some time and summarize the article: something happened 4bn years ago, it possibly created RNA, it might have created DNA after or concurrently (we don't know) and we definitely have no clue about how genetic code was formed, but it must have been done a long long time ago because it is the same on all life. The end.

singularity2001• 2 years ago

it might've come from outer space which only shifts the question and we still have no idea

photochemsyn• 2 years ago

The free-living ribosome hypothesis of the origin of life seems the most likely, was introduced over a decade ago, and isn't even mentioned in this article.

The basic idea is there wasn't an RNA world or a protein world, but that abiotic genesis of nucleic acid and amino acids took place concurrently, and those entities (which may have formed short polymers) organized into various structures based on the well-known amino acid / nucleic acid association mechanisms (based on hydrogen bonding).

Somehow, this proto-ribosomal-association developed the ability to self-replicate. Ribosomes today are engaged in the process of linking one amino acid to another using an mRNA template as the blueprint (and a complex association of amino-acid binding tRNAs which 'read' the mRNA template, and a suite of enzymes that correctly link tRNAs and amino acids, the critically important amino-acyl tRNA transferases.). In the origin-of-life model, the protoribosomal RNA becomes the very first functional RNA to self-replicate, but it's already associated with abiotically formed amino acids (a much smaller set than what life uses today). It's something like a virus that can self-replicate without any help from a cell.

Practically, this means the earliest ribosomes must have also been RNA polymerases, an activity which later was separated into a separate entity by evolutionary processes.

Even if you can make something like this in a lab [1], it doesn't really 'prove' that this is how life started, there might be multiple different routes to a living self-replicating cellular entity, but time and evolution have erased much of the evidence.

As far as the origin of DNA, the main benefit is having two copies of the information which allows for error-correction, and the disadvantage is having to translate the DNA to mRNA to feed to the ribosome to make the proteins, so perhaps it took place after cellularization

[1] "The Ribosome as a Missing Link in Prebiotic Evolution" Root-Bernstein & R-B

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6337102/

rolph• 2 years ago

'primordial' chemistry, such as deepsea geothermal vent locations. the abiotic synthesis of ribose related compounds start it all up.

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

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

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

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

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023395/

miohtama• 2 years ago

For panspermia theory (the life originated from the space) you need to remember that universe itself has evolved. There was early time in the universe when it was so warm that liquid water was possible “everywhere”. Though this does not solve anything, just shifts the starting point and conditions somewhere else.

baruz• 2 years ago

A G Cairns-Smith postulated that self-organizing, growing silicate crystals could have formed a substrate against which organic molecules would pattern themselves until they eventually began self-replicating on their own.

jacknews• 2 years ago

"and finally, self-copying RNA formed."

LOL, do we have an example of such a thing, RNA that can copy itself independently, without helper chemicals/energy?

It's quite clear to me that life most likely started with a 'co-operating set' of chemicals that could catalyse each other's reactions, necessarily in the presence of some kind of energy gradient, and that RNA, DNA, etc came after, and even then still rely on the 'soup' of chemicals that they are in, for reproduction.

pfdietz2• 2 years ago

There’s also no oxygen or ozone layer, leaving the planet’s surface exposed to the sun’s intense UV rays and making it blisteringly hot.

The Sun has increased in brightness by 30% since it settled onto the Main Sequence, so press X to doubt the "hot" part.

coolhand2120• 2 years ago

So, it seems reasonable to expect that the building blocks of life formed spontaneously

Why on earth is that reasonable to expect?! That has to be the most anti scientific thing possible. “We tried really, really hard in a lab under carefully controlled conditions and couldn’t make it happen therefore it must just happen spontaneously!”

And that’s what passes for mainstream science? I think this article is secretly trying to convert people to alien origin or creationism the way they argue this point.

Where did DNA come from?

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