Where did DNA come from?
geneticsunzipped.com
geneticsunzipped.com
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)1: "Trusting Trust" by Ken Thompson https://users.ece.cmu.edu/~ganger/712.fall02/papers/p761-tho...
RNA: asm text file
Protein: compiled binary
also: t-RNA is a hybrid of RNA and amino acids, which is like a hash table
RNA is the start of everything (see: RNA world)
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.
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.
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.
Of course you can model various aspects of cells mathematically. But that doesn't require any analogies to software.
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.
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.
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."
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.
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.
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.
What terms/concepts should be used in their place?
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.
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...
Importantly, and still relevant to modern day life is the fact that metabolic states contain information and themselves can be heritable.
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.
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.
Can Biology Be Reduced To Physics? — https://youtube.com/watch?v=A4yzK-8OGtc
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.
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.
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://en.wikipedia.org/wiki/Abiogenesis
https://en.wikipedia.org/wiki/Assembly_theory
https://en.wikipedia.org/wiki/Pentose_phosphate_pathway
The Sun has increased in brightness by 30% since it settled onto the Main Sequence, so press X to doubt the "hot" part.
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.
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.
No. They can be separated by temperature alone. See DNA denaturation phase during Polimerase Chain Reaction.
Just because you know how a car works doesn't mean that you can't enjoy a ride across the countryside.
sure, some times it's more difficult to suspend disbelief, but on the other hand there is many more details that can be appreciated only by people who know how difficult they are to pull off, and are completely missed by people not in the know.
/s aside - fair point, well spotted.
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.