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Comment by taxerbee1 | Hacker News Reader

A new study published in the journal Nature sheds light on the evolution of complex life from newly discovered "Asgard Cells"! Go science... love the science of evolution, so fascinating!

So it seems like these Asgard Cells are complex cells that evolved on Earth over 1.8 billion years ago. These cells have features similar to both bacteria and eukaryotes, which are the two main types of cellular life on Earth. The discovery provides insight into the evolution of eukaryotic cells, which are believed to have originated from a symbiotic relationship between two different types of bacteria. As we go further and further back in time, chemical and biology evolution merges :)

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Not quite, they have features of similar both typical archaea and eukaryotes, but living in close symbiosis with bacteria. We already pretty much knew that eukaryotes came from an archaea/bacteria merger, we're just much closer to figuring out how that happened.

Where did the entropy in the genome of any species come from? The data man, where did it come from?

When everything in the universe degrades or rusts or tends towards decreasing complexity.

Edit: When I say entropy the first time I'm referring to algorithmic information theory entropy, whereas the second indirect reference is to physical entropy.

I would encourage you to find a copy of (it's very expensive, but there are methods to acquire it, such as "libraries") Eugene Koonin's "The Logic of Chance", if this is a topic you're interested in. It basically goes through evolution from a molecular biology and information theory standpoint (and culminates in his own theory of "genesis").

It seems to be available for download for free? 1st or second hit on google:

http://www.evolocus.com/Textbooks/Koonin2011.pdf

Awesome! It wasn't the last time I checked.

I remember exploring a "traditional html with images" website about natural selection (I don't think it was interactive, but I do think the source code for each experiment was provided). I assume it was made by a mathematician / physicist. Do you by chance happen to know which site I have in mind? I (vaguely) recall a blueish gray background.

Thank you, you are the only person that actually addressed my point in this thread. I just acquired the book.

It came from the energy that the Sun pumps into the system.

I don't know why so many people forget that the laws of thermodynamics are all about closed systems, which the Earth is very much not.

This is not, in general, a compelling answer. It's true that the second law is a red herring, but it remains true that in any system humans have measured, including open systems, huge gobs of complex information like even the simplest life do not spontaneously form. Saying "it's an open system, dummy" ignores this gap. The truth is we still haven't quite figured it out. We're getting there (Jeremy England's work is the big one in my mind), but we're not there yet.

Even if the Earth was, the environments where life evolved very much are not. Vulcan and chemical processes are going to add and take away energy and matter from the molecular system that evolved into life.

I don't know why so many people forget to explain where _the complexity_ comes from and just drive right off the road assuming I don't know something basic and can distract from having to answer the real question about the complexity of the information in DNA and its origins. Not a very generous argument style you have there.

The question you are asking isn't a valid question, because it's based on the faulty assertion that "...everything in the universe degrades or rusts or tends towards decreasing complexity". That's just not true. And given you think it's true, the belief that you don't know something basic isn't an assumption.

There isn't a way to answer questions based on faulty assumptions, like "Why did you murder JFK?" People have actually been quite kind in giving you "sort of" answers such as "It came from the energy that the Sun pumps into the system."

I'll also point out that when people make the faulty assertion that everything tends toward decreasing complexity, they usually try to follow up with some intelligent design argument. You haven't done that in this post, but that is probably why you're getting answers that are a bit guarded or combative, because people are prepared for you to take this discussion to a truly ignorant place.

Have you never heard the joke about a million monkeys typing on a million towers eventually producing the complete works of Shakespeare? Little by little variation is accumulated when it’s beneficial, and the organism dies fast when it’s not.

This is also a bad argument. You probably know very well that if a cryptographer can force you to employ infinite monkeys on typewriters to guess their key, they'll declare victory. You need a mechanism that searches and focuses the space of possible chemistry, that forces life into being. If you look at the timeline for the emergence of life, I don't think it's one that supports an infinite monkey type of mechanism. It was too fast.

> You need a mechanism that searches and focuses the space of possible chemistry, that forces life into being.

That's exactly what the infinite monkeys on a typewriter are a metaphor for.

In literal terms, it's trillions of trillions of protein reactions happening along earth's coastlines.

> If you look at the timeline for the emergence of life, I don't think it's one that supports an infinite monkey type of mechanism. It was too fast.

If it literally was infinite monkeys, we'd expect life to emerge near-instantaneously.

The reality is, of course, that it's not "infinite monkeys" but "a whole f-ing lot of monkeys"--the question is whether it's enough monkeys to produce life in the timeline. There's a lot of research that's been done on this, and we have pretty good data. I'm not an expert in this field, but my outside impression from the research I read is that the open question at this point is actually not why it happened so fast, but why it didn't happen faster. If you're actually interested in the numerical justifications for the timeline, the research is pretty well documented, but given you've ex-nihilo declared that the timeline is too fast, I suspect you aren't actually curious, and are instead leading into an argument you want to make.

My read of the timeline is that life emerged very soon after it was physically possible for it to exist. I'm interested in research wondering why it wasn't even faster. What should I search for?

My point is, "infinite monkeys" (as a metaphor, taking them literally is a strawman) describes a brute-force approach. I don't think a physical process that randomly smashes together, say, long RNA molecules will actually result in life, certainly not quickly, probably not at all. The combinatorics of long strings are prohibitive. I think some selection process needed to take over sooner.

I don't know if that's the argument you think I "wanted to make". As far as I'm concerned I've said exactly what I mean, just longer and more explicit for a hostile audience this time.

> My read of the timeline is that life emerged very soon after it was physically possible for it to exist. I'm interested in research wondering why it wasn't even faster. What should I search for?

It's been a while since I researched this, and now I'm trying to search with similar terms to what I used before and it's not working. The reason seems to be that there's a ton of fluff papers about life on Mars and other planets: this sort of speculative modeling isn't without value, but it's lacking much hard evidence, unlike the papers I was reading a decade ago which had a ton of geological information. It's frustrating. I wish I could point you at something good here, if only so I could find stuff for myself again.

> My point is, "infinite monkeys" (as a metaphor, taking them literally is a strawman) describes a brute-force approach. I don't think a physical process that randomly smashes together, say, long RNA molecules will actually result in life, certainly not quickly, probably not at all. The combinatorics of long strings are prohibitive. I think some selection process needed to take over sooner.

Well, two things:

Proteins aren't like cryptographic keys, and I'd encourage you to abandon that way of thinking about them. Finding a single cryptographic key is like finding a needle in a haystack: there's only one key that works. But with proteins there are a lot of combinations that work, and even "work" is a bit hard to define because there are a lot of proteins that aren't RNA or DNA, but exhibit lifelike properties. Some of these proteins are very combinatorially simple compared to DNA. So far I don't know of any research that connects a specific prion with a theorized route toward more complex structures (these seem to have evolved in the context of larger organisms) but it at least shows us that very simple proteins can exhibit lifelike properties. Put another way, partial answers count. So instead of a needle in a haystack, it's a haystack with a bunch of needles, and bits of metal that aren't really needles but count as needles.

2. And keep in mind it's not just the problem space that's large: the amount of "processes" doing the searching is also large.

My point is, I don't think it's evident that the combinatorics of long strings are prohibitive, given that there are many "right" answers in the search space, and some partial answers count.

To actually put numbers on this to say how long it would take would require information I simply don't have, but I'm skeptical that you have that information either.

I don't think of proteins as cryptographic keys. But monkeys-on-typewriters thinking is more closely aligned with cryptography than biochemistry. That's kind of my point.

As posted in earlier articles and from what I have read: The basic buildings block of our life spontaneously form from the chemistry of the early Earth (our even the chemistry of space). Lipid membranes spontaneously form enclosed structures. This forces molecules together allowing fast and directional catalysis. RNA is directly catalytically active on itself and other molecules.

That's just what I can recall. There's more about DNA/RNA and amino acids pairing, but I can't remember it off the top of my head.

Lipid membranes are pretty cool, but they're not life. Nucleobases and amino acids are letters, not sentences.

I understand we aren't a closed system.

But that still doesn't explain to me where the complexity came from.

> I understand we aren't a closed system.

Just because you can parrot the phrase doesn't mean you understand it. Your statement " everything in the universe degrades or rusts or tends towards decreasing complexity", which simply isn't true for a local subsystem such as the earth, demonstrating that you do not understand what it means for Earth to not be a closed system.

> But that still doesn't explain to me where the complexity came from.

It comes from energy from the sun forcing trillions of trillions of proteins together at random all along the earth's coastlines. The proteins, forced together, are more complex than the previous molecules. Most of them are unstable, but even a one-in-a-billion chance of forming a stable protein is almost guaranteed to happen when there are trillions of trillions of reactions occurring.

That lacks explanatory power. It is a hand wavy process. "Random movements caused by the sun". By what method of action? Tell me exactly. You can't because you don't know. You are just too arrogant to admit it.

1. It's strange that you've put quotes around something I didn't say.

2. I said a lot more than what you put quotes around, which explains the method of action. If you want more specific information, you'll have to engage enough with what I've already said to ask a more specific question. I won't waste my time explaining parts I've already explained and you've ignored.

You talk about the physical process, but not where the information came from. Information only comes from consciousness.

If you think randomness created dna with a specific function I have a bridge to sell you

> Information only comes from consciousness.

Ah, there it is, the total nonsense I was expecting.

That's not even a coherent scientific claim: it's not provable or disprovable because you can't even clearly define half the words. You're just saying things with no evidence because they were told to you.

Next time, save everyone some time and just make your argument for creationism up front without asking questions as if you were interested in answers. This whole pretending to ask questions thing you did here was dishonest.

Bye.

Ultimately this question is the question of why the universe isn't completely isotropic in all directions with a completely uniform distribution of matter and energy. To the best of our knowledge this is due to quantum effects at the beginning of time creating a temporary asymmetry whose resulting "sloshing" created everything more complicated than evenly-distributed hydrogen gas. Life on earth is the tiniest swirl of complexity in the vast waterfall of "wasted" entropy that is the sun burning out.

>Ultimately this question is the question of why the universe isn't completely isotropic in all directions with a completely uniform distribution of matter and energy.

I don't think it's a self-evident given that going against the grain of increasing entropy leads to complexity. The obvious but naieve opposite of increasing entropy is going towards something like relatively simple crystal structures.

That is rather hand wavy and doesn't explain where the complexity in DNA comes from, you just swept that problem under the rug with a blanket explanation that lacks explanatory power.

"Complexity" is not a magic force that must be conserved. In any system that has both an energy gradient and a path for that energy to travel that is not isotropic, complexity will emerge as entropy increases. That holds whether the system in question is a pool of water with a bumpy downhill slope or an entire ecosystem.

https://theconversation.com/emergence-the-remarkable-simplic...

DNA is actually rather simple. It basically consists of about the fewest number of bases possible for encoding information (four), even though more bases are possible (and have been stably engineered into organisms). Even so, while these bases pair off well, there is some cross-talk possible (G-quadruplexes, G:T base-pairing).

Stir some milk into some coffee and just shortly after they make contact but well before it's even half way to being completely mixed, ask yourself where does the complex structure come from?

https://www.teepublic.com/t-shirt/22098576-complexity-and-en...

The only question is where the first self-replicating structure came from. As soon as you have a self-replicating structure, you have evolution. Evolution is driven by these self-replicating structures competing for the available energy. A more efficient replicator outcompetes its less efficient siblings at exponential speed. If more complex replicators are more efficient, then complexity evolves naturally. It's basically stochastic gradient descent, with the environment as the training data, and replicator efficiency as the objective function. Evolution prunes all the inefficient branches, and what remains may seem hand-crafted, but in fact it's just what remains after everyone else got outcompeted.

Now, the question is whether the first replicator can arise randomly from the primordial soup or not? Was the first such replicator simple enough to be spontaneously assembled from random inorganic molecules floating in water? I think on a long-enough timescale, the answer is yes.

> As soon as you have a self-replicating structure, you have evolution.

Not quite, you also need the replication to have random errors.

Even crystals have random inclusions. Catalysis and replication without error is harder to achieve than catalysis or replication itself.

On a DNA/RNA level, various nucleotides have affinity not only for their normal partner, but less so for other partners. This becomes especially important as environmental damage (from the energetic systems we all live in) cause alterations in the chemical structure of the nucleotides. That's just one method of mutation.

And the energy from within the earth through geothermal vents

It comes from Death's sickle, prunning the random noise introduced by mutations to generate useful information. Natural selection. There's a paper where people put bounds in terms of bits/generation a species can acquire over time. Apparently sex developed as a workaround life found to inclease this bandwidth from about 1 bit/generation to much larger values: http://www.inference.org.uk/mackay/gene.pdf

Randomization plus selection.

The big innovation of life is having a form of matter that can quine its own arrangement. Once you have that, the complexity that ensued was predictable.

Life it's just a cooler way to speed up entropy.

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