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)

“Von Neumann Architecture”

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.

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...

Yes but always human in the loop. I mean a self replicating, source modifying program.

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

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

> 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.

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."

On the other hand, you can criticize evolution without being a young earth creationist.

What are the proper qualifications to criticize evolution?

I have no idea, I just know that not everyone who criticizes the theory is a young earth creationist.

True, there's a whole taxonomy of completely discredited schools of thought adjacent to young earth creationism but different in their respective details.

Lol, you are so biased

'Bias' means a lot of things to a lot of people. I'm perfectly comfortable being called biased against criticisms of the modern synthesis, which is not the dig that you seem to think it is. I would reject the idea that I'm biased in the sense of predisposed to unfairly reject a legitimate idea due to pre-existing ideological commitments, but I suppose the devil is in the details on that one.

Suffice to say I don't think critics of evolution are rehabilitated into respectability just by noting that there are other forms than young earth creationism.

Supporting the modern synthesis is the most boring thing you can do. No significant scientist has ever become famous for doing that.

I don't see how that has anything to do with anything. Perfectly happy to be boring.

It's not just boring, it's almost certainly wrong. If you're going with the mainstream consensus just because it's the consensus, chances are almost 100% that you are wrong. The history of science proves this. At any given moment we only see one small facet of the truth, and we need real thinkers (not sheep who just echo "consensus") to reveal other facets. Your attitude impedes scientific development.

See Wronger Than Wrong by Isaac Asimov, which is about this exact argument:

>When people thought the Earth was flat, they were wrong. When people thought the Earth was spherical, they were wrong. But if you think that thinking the Earth is spherical is just as wrong as thinking the Earth is flat, then your view is wronger than both of them put together.

>According to John Jenkins,[4] who reviewed The Relativity of Wrong, the title essay of Asimov's book is the one "which I think is important both for understanding Asimov's thinking about science and for arming oneself against the inevitable anti-science attack that one often hears – [that] theories are always preliminary and science really doesn't 'know' anything."

https://en.wikipedia.org/wiki/The_Relativity_of_Wrong https://en.wikipedia.org/wiki/Wronger_than_wrong

I agree with Asimov. And the point stands, that you are almost certainly wrong.

But how wrong? And more importantly, do you understand why that is an important question?

Dismissing the achievements of present-day science by appealing to the wrongness of the past -- to imply we are just as wrong now as we were then-- is to exhibit the very form of ignorance that Asimov was criticizing.

Well, you could start by reading these books:

1. Darwin on Trial by Phillip E. Johnson

2. The Stairway To Life: An Origin-Of-Life Reality Check by Tan & Stadler

3. Darwin's Doubt by Stephen C. Meyer

Before you pick up a copy of Darwin's Doubt to learn about evolution, you should probably know the subtitle is "The Explosive Origin of Animal Life and the Case for Intelligent Design."

I see Meyer being favorably cited here, but his two major books have been pretty firmly rejected by real scientists from everything I have seen.

To the extent Meyer has been able to garner positive critical reception, it has been an in-between nether space of media, book reviews, and unfortunately academic philosophy. I actually would go so far as to say that folks like Nagel offering positive commentary on Meyer is an indictment of Nagel and a perfect illustration of how his school of anti-reductionist skepticism can go completely off the rails.

Are you implying Meyer isn't a real scientist?

Openly stating. He was educated as a philosopher with a PhD in 'history of science.' His entry point to conversations on biology is from the perspective of a historian of science.

He also has a degree in physics and worked as a geophysicist for four years.. I'd say he is more educated in scientific matters than most people. Maybe including yourself?

From the google, I see that was a bachelors from 1981 to go into the private sector for work that had no connection to any scientific career.

What qualifies someone as a 'scientist' can be a fuzzy continuum, but that's on the weaker side of the spectrum. Especially for someone who isn't a biologist going against the mainstream consensus of biology.

And what is your degree in?

You could, but you shouldn't. Picking up any basic science book would be better use of your time.

Those are by people not qualified to criticize evolution.

I'm not sure about the others (don't know who they are), but Meyer certainly is.

What exactly are his qualifications? He has no degree in biology. Does he perhaps have a PhD in intelligent design?

He has master's and doctorate degrees from Cambridge in philosophy and history of science, and a bachelor's in physics, as well as having worked as a physicist for several years. He has also done extensive research on the issue and done lots of publishing on it. He's more qualified than almost any Hacker News poaster.

Every ounce of his scholarship has been firmly rejected by the scientific community at every step of his career. Any HN poster is perfectly qualified to assess his credentials and claims relative to those of the academic mainstream.

Edit to reply to comment below: Meyer himself agrees that it is in fact true, and would be the first to affirm that he has faced pretty stiff rejection by the scientific mainstream on questions of biology. One of his major talking points is his feeling that he's been ostracized from the scientific community. He would not agree with anyone claiming it's "not true" that he has clashed with modern scientific consensus.

This just isn't true.

Of course it is.

Not in regard to evolution.

> 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.

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.

Swerving into religious flamewar is not a good move either. Please don't do this on HN.

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.

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.

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.

"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.

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.

How exactly is the analogy "DNA: file.c" helpful to answer the question from the article "Where did DNA come from?"?

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.

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.

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.

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

What terms/concepts should be used in their place?

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.

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...

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.

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