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)
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.
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.
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
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!
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.
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.
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.
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."
True, there's a whole taxonomy of completely discredited schools of thought adjacent to young earth creationism but different in their respective details.
'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.
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."
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.
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.
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.
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."
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.
> 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.
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.
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.
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.
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.
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.
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.
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.
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.
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"
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.
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.
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
> 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.
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.
> 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.
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.
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.
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.
yeah, it's like saying directors can't enjoy movies, since they know how they're made.
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.
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.
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).
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.
The slippery slope of DEI .. it starts by recognising the contributions of women and before you know it the wokerati are giving credit to .. graduate students!!
I am a theist. I also find what you are saying pretty unconvincing.
Panspermia theory means there’s basically no bounds on how long ago life may have formed or how many trillions of planets may have hosted primordial soup waiting for the right interactions. Good statical analysis and biochem showing that it couldn’t have formed on earth would be better evidence for panspermia than divine genetics.
The universe and our existence is plenty awe inspiring to me. I don’t need to invent miracles or fit the evidence to the conclusion. I think it’s better to use our intellect and see where the evidence leads us rather than pre-supposing the nature of God.
Panspermia gets you nowhere and merely allows you to try to save face before what you suppose are your more sophisticated colleagues.
Also, "no bounds on how long ago life may have formed" just displays ignorance of the fact that we do in fact have bounds on the age of the universe.
It is obvious to me that you have ruled miracles out by definition, allowing you to conclude that miracles must not have occurred. Forgive me for rolling my eyes.
There are single proteins that are so complex that the search space for them is so large that it would be equivalent to picking a single specified elementary particle out of all the elementary particles in the Universe. Also, the shape of a protein is like a combination lock -- you have to get it right or it just doesn't work and also gives you no feedback that you can use to make a better guess.
Also, why are you a theist? Do you hear God talking to you or something like that?
Most people are atheists, because the concept of god was created to explain the world when humans did not have enough knowledge and information for scientific analysis, but this is not the case anymore today. Over centuries, this went away due to inventions of printing press, literature, a lot of basic scientific research and so on.
Also if you read the article it gives you multiple theories how initial proteins formed. No god needed there.
You appear to be attempting to make a God-of-the-Gaps argument, but you are unaware that "scientific progress" is widening the gap when it comes to the origin of life question.
For example, in Darwin's day it was assumed that the cell was a simple blob containing life-force, but now we have powerful electron microscopes and it turns out that our initial assumptions about how simple life must be were completely wrong.
And yes, I read the article. I've read many such articles. There are a lot of "theories" out there, but none that pass the smell test, although most of them try to snow the unsophisticated reader with a bunch of acronyms and jargon.
I downvoted you but I'm not a sophomore. My background in this field includes a PhD dedicated to studying DNA, and postdoctoral work studying evolution. I downvoted you not because I think you're wrong (I have no real opinion about supreme beings or creators with respect to the universe) but because you didn't form a convincing argument, and then just sort of insulted people's intelligence if they don't agree with you.
I wasn't referring to literal sophomores in college, but rather I was using the term metaphorically to mean "a person who has gained a little knowledge but now thinks they have a deep understanding." I understand that you have a PhD in DNA!
