[HN Gopher] Where did DNA come from?
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Where did DNA come from?
Author : andsoitis
Score : 80 points
Date : 2024-02-12 03:21 UTC (1 days ago)
(HTM) web link (geneticsunzipped.com)
(TXT) w3m dump (geneticsunzipped.com)
| panja wrote:
| There are some mysteries I don't think we'll be able to solve and
| that makes me sad
| bregma wrote:
| It makes me glad. One's reach should always exceed one's grasp.
| Keep searching.
| alas44 wrote:
| "The mystery of life isn't a problem to solve, but a reality to
| experience." Frank Herbert
| exe34 wrote:
| 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 wrote:
| If you take the view that existence is physics and physics is
| math, then doesn't this follow from Godel's incompleteness
| theorems?
| msla wrote:
| No, it doesn't, at least when applied to physics.
| verisimi wrote:
| A: Watson and Crick
| defrost wrote:
| Photograph 51, by Rosalind Franklin (1952)
| dekhn wrote:
| Actually taken by Raymond Gosling, not Franklin.
| Faaak wrote:
| 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 wrote:
| 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
| genman wrote:
| It (the first in the list) is a very nice and empowering
| write-up. Thank you for sharing it.
| dekhn wrote:
| 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 wrote:
| 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 wrote:
| > Biology is applied physics.
|
| _Can Biology Be Reduced To Physics?_ --
| https://youtube.com/watch?v=A4yzK-8OGtc
| genman wrote:
| 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 wrote:
| > [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.
| tetris11 wrote:
| 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)
| willis936 wrote:
| 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.
| tetris11 wrote:
| 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...
| willis936 wrote:
| Yes but always human in the loop. I mean a self
| replicating, source modifying program.
| fxj wrote:
| 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
| Faaak wrote:
| 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 wrote:
| "Von Neumann Architecture"
| getoffmycase wrote:
| 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 wrote:
| > _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.
| fabian2k wrote:
| I don't think the programming analogies are helpful here,
| they seem to cause a serious amount of confusion. The basic
| idea isn't so bad, but too many people seem to try and push
| them much, much further than they can work.
|
| For a developer this analogy also implies a lot of
| assumptions that they know to be true for code that are
| simply wrong for biology.
| theGnuMe wrote:
| One can view the cell as an information processing
| entity. If we agree with that view then it can be
| analyzed as an abstract computational process.
|
| If you are upset about using the word 'computational'
| then consider it to be a dynamical process. We can then
| use mathematics to analyze this system.
|
| In any event, genes (programming instructions) encode
| proteins (applications) that run in the cell (operating
| system).
|
| Now biology is weird and has multiple feedback steps,
| some of which we probably do not even know yet, but the
| basic approach is solid.
| fabian2k wrote:
| Those analogies imply things that simply aren't true.
| Genes and proteins aren't digital, they are real entities
| with physical and chemical properties that affect
| everything they do.
|
| Of course you can model various aspects of cells
| mathematically. But that doesn't require any analogies to
| software.
| theGnuMe wrote:
| There's no requirement that a computer or computational
| process be 'digital'. Analog computers exist, in fact,
| the first computers were analog.
|
| At any rate digital (0,1) strings aren't that different
| than DNA strings (A, T, C, G) and just because we have 4
| characters in the alphabet doesn't mean you can't analyze
| it as an abstract computational process.
|
| You can also discretize the concentration of molecules
| such that above a threshold switch like behavior occurs
| (gene turns on or off).
|
| Also people have done experiments where they program DNA
| to perform computations to solve various problems like
| the traveling salesman problem. This is a direct
| application of using biology to solve a "digital problem"
| https://www.nature.com/articles/news000113-10
|
| So here we have an example of an artificial logical
| problem encoded into DNA and solved using biology. That
| means biology can simulate computational algorithms.
| FrustratedMonky wrote:
| "model various aspects of cells mathematically"
|
| I think a lot of people here will equate
| software/programming to mathematically modeling.
|
| Saying you can model/math it, but not use software
| analogies, is just really trying to split hairs, since
| models/math is also software.
| getoffmycase wrote:
| The fundamentals of biology are not difficult to grasp.
| Evolution, DNA -> RNA -> Protein, basic cell signalling,
| etc are all really easy to grasp with just the tiniest bit
| of effort. There's really no place for bad analogies,
| especially such a misleading one.
|
| Sorry to bite your head off, but the reason that I'm
| passionate about this topic is, and I'm not joking, young
| earth Creationism. An analogy like the grandparent is
| something simple to grasp by many people, and then the
| Creationists can quickly turn around and say, "Well you see
| how biology is like a computer; somebody built a computer;
| therefore, God created us in six days, 6000 years ago."
| simpletone wrote:
| > The fundamentals of biology are not difficult to grasp.
|
| The fundamentals of biology are extraordinarily difficult
| to grasp. Not only that, the fundamentals aren't set in
| stone and are subject to change. The rise of epigentics
| being a recent example. The only people who claim the
| fundamentals are not to difficult to grasp are people who
| have a superficial and incorrect understanding of it.
|
| > Sorry to bite your head off, but the reason that I'm
| passionate about this topic is, and I'm not joking, young
| earth Creationism
|
| So you got triggered because you have a political agenda?
| It's my experience that people who know nothing argue
| with or feel threatened by creationists. I say this as an
| atheist.
|
| > "Well you see how biology is like a computer; somebody
| built a computer; therefore, God created us in six days,
| 6000 years ago."
|
| The biology-computation analogy has been used since the
| founding of computer science. Everyone from Turing to the
| commenter you attacked has used it. Heck, even biologists
| view biological systems are biological machines.
|
| You are fundamentally no different than the creationists
| you argue with. I'm almost certain you know nothing about
| biology or computer science other than pop culture
| nonsense.
| dang wrote:
| Please don't post in the flamewar style to HN, no matter
| how wrong someone is or you feel they are.
|
| Also, please edit out swipes from your comments.
|
| Both these points are in the site guidelines:
| https://news.ycombinator.com/newsguidelines.html. If you
| wouldn't mind reviewing those and sticking to them when
| posting here, we'd appreciate it.
| dang wrote:
| Swerving into religious flamewar is not a good move
| either. Please don't do this on HN.
| Viliam1234 wrote:
| How exactly is the analogy "DNA: file.c" helpful to answer
| the question from the article "Where did DNA come from?"?
| Ralfp wrote:
| 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.
| tivert wrote:
| I've also heard this described as "Engineer's Disease": "We
| think because we're an expert in one area, we're
| automatically an expert in other areas."
| (https://news.ycombinator.com/item?id=10812804).
|
| I think the core lazy assumption that enables is the idea
| that all the other fields are properly understood as just
| like your field. Sometimes it's so bad that a software
| engineer will outright dismiss the ideas of actual experts
| as misguided, and insist on some "disrupting" the fields
| with some half-ass software-thinking.
| jibal wrote:
| 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.
| FrustratedMonky wrote:
| Is there an alternative to analogies and metaphors when using
| language?
|
| What terms/concepts should be used in their place?
| dekhn wrote:
| 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.
| dang wrote:
| 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.
| ..
| UniverseHacker wrote:
| 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.
| theGnuMe wrote:
| Nice, it's amazing how the analogy matches up so well.
| UniverseHacker wrote:
| 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.
| pfdietz wrote:
| 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 wrote:
| 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.
| UniverseHacker wrote:
| 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 wrote:
| > 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 wrote:
| 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 wrote:
| Midichlorians are the power house of thw cell.
| utopcell wrote:
| 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 wrote:
| it might've come from outer space which only shifts the
| question and we still have no idea
| photochemsyn wrote:
| 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 wrote:
| '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 wrote:
| 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 wrote:
| 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 wrote:
| "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.
| pfdietz wrote:
| > 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.
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