The RNA World Hypothesis

https://www.ncbi.nlm.nih.gov/books/NBK26876/

by PaulHoule • 5 years ago

146 34 5 years ago

ncbi.nlm.nih.gov

COGlory2• 5 years ago

If anyone is interested in further reading on this topic, or on evolution/origin of life in general, I highly recommend "The Logic of Chance" by Eugene Koonin. The book pieces together the latest knowledge from all the major fields of biology (genetics/bioinformatics, structural/physics, etc), math, physics, and philosophy in a way I've never seen done before. It interrogates virtually every hypothesis of the origin of life, from all possible angles, starting mainly with what is evolution and what are the possible routes to where we are, as well as their probabilities, and critique of applying probability to these models.

I'm admittedly biased, because Koonin is a personal friend and occasional colleague of a member of my PhD committee, but what I've heard from everyone that I know who has interacted with him (unfortunately I've never had the opportunity, to my great dismay), is that he's completely unassuming and carries no ego at all. My experience reading "The Logic of Chance" has confirmed this. The book is accessible to anyone with an ability to read. It taught me more about how to think for myself and recognize bias than probably any other work I've read (perhaps excluding Taleb's "Incerto" series, which complement Koonin's work very nicely), and also taught me a lot about evolution. The book can be found on the usual websites that graduate students are apt to visit.

The RNA world hypothesis is almost single handedly responsible for my interest in virology.

jacquesm2• 5 years ago

How is it simultaneously possible to be a personal friend to someone and not have had the opportunity to interact with that person?

COGlory2• 5 years ago

Sorry - run on sentences made it unclear. My mentor is the friend. I'm the one that's never interacted

changoplatanero• 5 years ago

looks like a good book. i wish it wasn't so expensive on amazon

AllegedAlec• 5 years ago

You might also like the work of Collizi and Hogeweg. They did some rather interesting theoretical work on RNA world hypotheses, particularly on the issue of the error threshold.

adrian_b3• 5 years ago

About virology, there is no doubt that the first RNA molecule was a virus.

All the popular presentations about the "RNA world" are either incomplete and/or logically inconsistent.

There certainly was a RNA world, in the sense of a world where there was no DNA, but only RNA.

However, there must have existed 2 stages of the RNA world, the later stage, when protein synthesis based on translation from RNA existed, like today, and also an earlier stage, when only RNA replication existed, but RNA did not perform any useful function for its host living being, but it was only a virus that was replicated using energy and molecular components from its host.

The fact that there are RNA molecules that can have a catalytic effect like enzymes, as mentioned in the article is completely irrelevant. If such catalytic RNA molecules had ever existed before the apparition of RNA replication, they would have immediately disappeared without living any descendants.

Only from the moment when some self-replicating RNA molecules has appeared, i.e. the first virus, we have some chain of nucleic acid replications, which has continued until today and all the existing nucleic acid molecules must be descendants of the first virus.

The first replicating RNA molecule required for its synthesis energy and molecular components, in the form of ATP and free nucleotides, which can condense into RNA.

So there must have already existed an equivalent of a bacteria, with metabolism using energy from the environment (i.e. dihydrogen with carbon dioxide and ionic gradients), which was already able to make ATP, which would have been needed to synthesize the polymers made by condensation, e.g. peptides. The apparition of the first RNA virus was an initially undesirable side-effect of using ATP to perform polymer condensations.

Because any memory molecule, like RNA, needs an already existing living being for its first replication, there must have been a stage prior to the RNA world, when there were self-replicating living beings, but without memory molecules.

The self-replication of a system does not need a memory, it can be "hard-wired", where there is a closed chain of chemical reactions where each reaction synthesizes a new component based on previous components and eventually the first component is synthesized from the last components.

However such a self-replicating system without a memory had extremely low chances of evolution, because any random change was almost certain to break the self-replication cycle, leading to death without descendants.

Only after the apparition of RNA, and especially after the later appearance of the RNA to protein translation mechanism, it became possible for mutations to accumulate and eventually create a variety of living beings.

While the first RNA must have been a virus, because diverting ATP and other useful internal components to the production of RNA molecules could not have been of any good for the host, some time after the apparition of RNA-based protein synthesis, some form of symbiosis between a host and some DNA virus must have created the ancestors of bacteria.

Sharlin• 5 years ago

So there must have already existed an equivalent of a bacteria, with metabolism using energy from the environment (i.e. dihydrogen with carbon dioxide and ionic gradients), which was already able to make ATP, which would have been needed to synthesize the polymers made by condensation, e.g. peptides. The apparition of the first RNA virus was an initially undesirable side-effect of using ATP to perform polymer condensations.

No, you're not postulating an RNA world here. The whole point of the RNA world (aka "RNA first") hypothesis is that the first life (self-contained, self-replicating particles) was RNA-based, and both proteins and lipid bilayers came later. If you argue that the first RNA was a virus that parasitized already existing organisms, then it's usually called a "metabolism first" hypothesis.

usrbinbash6• 5 years ago

and also an earlier stage, when only RNA replication existed, but RNA did not perform any useful function for its host living being, but it was only a virus that was replicated using energy and molecular components from its host.

And in this stage, where there is no DNA, what molecule carried the genetic information of these host organisms?

Because any memory molecule, like RNA, needs an already existing living being for its first replication

No, it doesn't. RNA is capable of folding into complex catalytic machineries same as polypeptide chains (aka. proteins). An RNA synthetase itself composed of RNA is absolutely probable.

ramraj074• 5 years ago

You and I were probably the only folks who recommended this book in HN history so hi! Totally agreed that this is required reading for anyone interested in learning about modern science on evolution (as opposed to the Dawkins drivel)

xenophonf• 5 years ago

What's wrong with Dawkins (aside from him being an ass)?

kubanczyk• 5 years ago

I've looked on Google Books' preview and it reads quite smoothly.

I was surprised that Google's price is so much lower than Amazon's though? Less than a half? (Might be locale-dependent, I'm in Poland). It has been long since I bought anything on Google, but I assume it can still be converted to a DRM-free epub like described here?: https://www.reddit.com/r/kindle/comments/3menci/i_prefer_my_...

Where's the catch?

Yajirobe• 5 years ago

Don't order from Amazon, please. Don't support them.

Mezzie• 5 years ago

Converting the book files is dead easy; Calibre can make pretty much any format you want. I'm visually-impaired so I prefer eBooks, but screw DRM. If I buy a book, it's MY book. Screw Amazon too.

redwood• 5 years ago

Love the way you write--"It interrogates virtually every hypothesis" <-- terrific

joshquin• 5 years ago

Stated Clearly has a great video about the RNA world hypothesis (https://www.youtube.com/watch?v=K1xnYFCZ9Yg) if anyone's looking for an engaging overview.

scrollaway• 5 years ago

That was a fantastic video. It gave intuitive explanations to not just the hypothesis itself but how certain biochemical mechanisms function. Thanks for linking it.

fwip• 5 years ago

This is from 2002, the title could probably include that.

java-man• 5 years ago

[0] Self-Sustained Replication of an RNA Enzyme, Tracey A. Lincoln and Gerald F. Joyce

https://www.researchgate.net/publication/23766369_Self-Susta...

ramraj074• 5 years ago

I have no doubt that our life originally evolved from an RNA world. I’m just not convinced the world is earth. This shit could not have happened so fast (few tens or hundreds of million years?) the moment it became conducive on earth. It must have flown in as archea from elsewhere!

Also anyone who’s worked in a lab trying to keep some Lb plates sterile would immediately see how difficult it would be to keep an earth sized Lb plate sterile if the galaxy has a ton of life harboring planets.

guerrilla• 5 years ago

Also anyone who’s worked in a lab trying to keep some Lb plates sterile would immediately see how difficult it would be to keep an earth sized Lb plate sterile if the galaxy has a ton of life harboring planets.

Unless you worked in an enormous vaccuum, I'm not realy sure how that's supposed to be comparable.

usrbinbash6• 5 years ago

This shit could not have happened so fast (few tens or hundreds of million years?)

It didn't happen that fast. The earliest direct evidence, (as in: fossils) for life on earth are 3.465 BILLION years old.

https://en.wikipedia.org/wiki/Earliest_known_life_forms

Also anyone who’s worked in a lab trying to keep some Lb plates sterile would immediately see how difficult it would be to keep an earth sized Lb plate sterile if the galaxy has a ton of life harboring planets.

The earths diameter is 12742 km.

A petri-dish is usually about 12 cm in diameter.

The closest star system (Alpha Centaury) is 9461000000000 km away (4.35 LY).

So the closest place in the galaxy where there is even sufficient mass for conditions to form life, is ~2970020405 earth-diameters from here.

Two petri dishes on opposite sides of the planet are ~106183333 petri-dish-diameters away from each other.

So purely from a perspective of distance, the chance that two petri-dishes on opposite sides of the planet transmit life between them, is an order of magnitude HIGHER than life coming to earth from outer space.

ramraj074• 5 years ago

Read your own ref. Optimistic estimates put the first appearance of life on earth as soon as 50 mill years after oceans formed.

The Petri dish analogy was only supposed to be tounge in cheek but if you want to be pedantic then consider that the medium between the source and destination is a frozen vacuum which means you have billions of years for transmission and spreading.

briancl• 5 years ago

I find it funny that the comments here split across:

“I have no doubt that life emerged from an RNA first world”

and

“I have no doubt that life emerged from a metabolism first world”

Last I checked, nobody should have absolute certainty for how life began. Progress comes from skepticism. Have more doubt!

pfdietz• 5 years ago

Given the instability of ribose even in plain pH 7 water, and the indiscriminate results of abiotic carbohydrate synthesis processes, I find the RNA-first hypothesis unlikely.

https://www.jstor.org/stable/2368016

usrbinbash6• 5 years ago

I do not doubt things just to doubt them however. Doubt has to be reasonable.

OliverJones• 5 years ago

The RNA World Hypothesis

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