6 ms·

That's pretty much the premise of the RNA world. I assume your actual question is why we don't observe RNA based lifeforms anymore. And the most likely explanat

by folli 6y ago

That's pretty much the premise of the RNA world. I assume your actual question is why we don't observe RNA based lifeforms anymore. And the most likely explanation is that this type of life form has a massive evolutionary disadvantage to currently existing life forms in terms of competing over resources and is extinct as the huge majority of all once existing species have gone extinct in the course of this planet's history.

sthnblllII 6y ago
Good point. See my reply to paulryanrogers
folli 6y ago
To add on to that (sorry, I think it's a very exciting topic): it's hypothesized that virions (a virus-like 'thing' that infects plants) are descendants of such RNA life that evolved to be parasitic.
- netcan 6y ago
  Interesting. That still doesn't give us any nonparasitic or non-symbiotic survivors. Merge with it, feed on it or go extinct.
ufo 6y ago
Another thing is that the current world is more hostile to RNA. Anyone who has ever worked with RNA will tell you that you need to be very careful during the preparation to avoid contamination with ribonuclease enzymes that degrade RNA. We're covered in them.
- tachyonbeam 6y ago
  It might just be that DNA has a better sweet-spot in terms of mutation probability, useful for evolution, and robustness, important for survival and transmission of useful genetic information.
- jonplackett 6y ago
  Is that an antiviral defense or something else?
  - deleted 6y ago
    [deleted]
- jiggawatts 6y ago
  This comment and its sibling is very interesting to me, because it's something I hadn't heard before. Why are ribonuclease enzymes so omnipresent? Is this the only reason why RNA is so difficult to work with, or are there other technical hurdles that are more difficult to overcome? Are we missing a big piece of the biological puzzle because of this? Any recent developments in this area?
  - keithwhor 6y ago
    RNA is a less stable molecule than DNA — it can be single-stranded, form double strands, self-pair (form loops), react readily with proteins... just difficult to deal with. On top of that, as mentioned, RNAses (enzymes that destroy RNA) are everywhere. Your skin secretes them as an anti-pathogen defense against viral RNA [0]. So do a plethora of other living organisms including single-celled bacteria ubiquitous in the atmosphere and on surfaces. I haven’t heard of any recent developments — it’s been a decade since I was in grad school and now I build software — but I briefly studied a subcategory of ribozyme called self-splicing group I introns which is where my interest comes from. [0] https://en.m.wikipedia.org/wiki/Ribonuclease https://en.m.wikipedia.org/wiki/Ribonuclease [1] https://en.m.wikipedia.org/wiki/Group_I_catalytic_intron https://en.m.wikipedia.org/wiki/Group_I_catalytic_intron
    - jiggawatts 6y ago
      > In addition, active RNA degradation systems are a first defense against RNA viruses, and provide the underlying machinery for more advanced cellular immune strategies such as RNAi. Huh... today I learned. I didn't realise we have such "low-level" immune defences, I always just assumed that the simplest defence we had were antibodies.
keithwhor 6y ago
In a sense we are RNA-based lifeforms. Our protein synthesis machinery is dependent entirely upon RNA. I think there’s a perspective here that the RNA world never disappeared, just became symbiotic with higher-order protein structures. On one hand, RNA viruses continue to replicate successfully (i.e. SARS-nCoV-2) and on the other we rely on rRNA, tRNA and mRNA to function as a highly-conserved part of cellular function across all organisms. When I was in grad school my default assumption was that ribozymes (catalytic RNA) are far more abundant than we currently know. RNA just very difficult to work with so there’s a selection bias against our ability to measure its behavior in vivo.
- wombatmobile 6y ago
  > In a sense we are RNA-based lifeforms. Our protein synthesis machinery is dependent entirely upon RNA. Yes, we are RNA organisms that have been incorporated into larger organisms, just as we are prokaryotes that have been incorporated into eukaryotes through endosymbiosis. https://evolution.berkeley.edu/evolibrary/article/_0_0/endosymbiosis_04 https://evolution.berkeley.edu/evolibrary/article/_0_0/endos...
  - keithwhor 6y ago
    Absolutely the comparison I was intending to convey! Biology is a messy and beautiful place filled with competition and cooperation. :) As much as 8% of our DNA was laterally transferred from viruses! In a sense, some infections result in a symbiosis with a host. https://en.m.wikipedia.org/wiki/Endogenous_retrovirus https://en.m.wikipedia.org/wiki/Endogenous_retrovirus
    - wombatmobile 6y ago
      Lateral DNA transfer is awesome. Check out this visualisation of the molecular apparatus assembled on the surface of a bacterium to inject a chunk of DNA into a neighbouring bacterium. Type 4 secretion system: ii- Pilus biogenesis https://www.youtube.com/watch?v=ihlFqOK5cZM https://www.youtube.com/watch?v=ihlFqOK5cZM
  - 6y ago
adrian_b 6y ago
A part of the hypothesis about the RNA world is correct, but all of it seems very unlikely. It is almost certain that DNA appeared later than RNA, probably in some kind of virus. Also, it is a logical necessity that the transcription of RNA into proteins, including the ribosomes and the transfer RNAs appeared only later than the replication of RNA. The part of the RNA world hypothesis that seems unlikely because it has very few supporting data is that the original biocatalysts a.k.a. enzymes were RNA molecules unlike anything that exists today. In my opinion, it is far more likely that the first enzymes were non-ribosomal peptides, somewhat resembling to parts of the proteins that constitute the enzymes of recent life forms. ATP and other nucleotides must have existed before RNA as a means to perform condensation (i.e. dehydration) reactions and the copolymerization of the nucleotides must have appeared as some undesirable side reaction, which somehow at some point generated some sort of self-replicating RNA, which was in fact the first virus, because its synthesis could not have any beneficial effects for the hosting life form. Only after the appearance of the transcription of RNA to proteins, the RNA could evolve into a source of components for the hosting life form so that RNA could change from a parasitic entity to an essential part. Life forms with RNA (and later with DNA) are analog with microprogrammable processors, because the nucleic acid molecules are memories which direct the synthesis of other components, so you can change the components by writing a different information in the memories, without changing the synthesis machinery. This kind of flexibility was certainly necessary for further evolution. Life forms before RNA are analog to hard-coded processors. Supposing that they were made with non-ribosomal peptides, there must have been a mechanism by which a complete life form was replicated, by a cycle of reactions were some kinds of peptides were assembled by other kinds of peptides. Non-ribosomal peptides exist even today in all living beings and they are assembled in the correct sequence from amino-acids without depending directly on the information stored in nucleic acids, like the proteins. Memories, like nucleic acids, are certainly not necessary for designing an ensemble of molecules able of self-replication, exactly like a memory is not necessary for implementing the control automaton of a processor. Nevertheless, it is likely that the further evolution of such a primordial life form was almost impossible, because all accidental changes in the structure of the component molecules would have resulted in a replication failure. After the separation of functions between a memory (nucleic acid) and a generic synthesis machine, evolution by changing the memory content became much more likely to be successful.
pfdietz 6y ago
A problem with RNA world is that RNA, and even ribose, is not very stable. It's not very plausible that the components of RNA could be present in pure forms that could allow faithful RNA replication, even ignoring energy needed for that.
- est31 6y ago
  RNA viruses do exist. After a certain length, the instability issues you point out cause problems, so usually they have a shorter genome. But I'd say that earliest life forms had shorter genomes anyways. Also, not every copy has to work out. You can see that with viruses, there are viruses where errors in manufacturing render most created viruses inactive.
  - pfdietz 6y ago
    RNA viruses exist. They exploit the highly "artificial" conditions inside living cells, where these unstable components are constantly being constructed and undesirable chemicals excluded. A primordial soup, without the precision enzymes and constant energy expenditure of this synthetic machinery, will be a grab bag of random glop. In Miller-Urey experiments the concentrations of any particular chemical decline exponentially with the number of atoms in that chemical. I believe ribose has never been seen in any such experiment (and certainly not in any but extremely low concentration), never mind the triphosphorylated nucleotides that provide the energy to drive RNA synthesis.

by folli 6y ago

sthnblllII 6y ago

Good point. See my reply to paulryanrogers

folli 6y ago

To add on to that (sorry, I think it's a very exciting topic): it's hypothesized that virions (a virus-like 'thing' that infects plants) are descendants of such RNA life that evolved to be parasitic.

netcan 6y ago
Interesting. That still doesn't give us any nonparasitic or non-symbiotic survivors. Merge with it, feed on it or go extinct.

ufo 6y ago

Another thing is that the current world is more hostile to RNA. Anyone who has ever worked with RNA will tell you that you need to be very careful during the preparation to avoid contamination with ribonuclease enzymes that degrade RNA. We're covered in them.

tachyonbeam 6y ago
It might just be that DNA has a better sweet-spot in terms of mutation probability, useful for evolution, and robustness, important for survival and transmission of useful genetic information.
jonplackett 6y ago
Is that an antiviral defense or something else?
- deleted 6y ago
  [deleted]
jiggawatts 6y ago
This comment and its sibling is very interesting to me, because it's something I hadn't heard before. Why are ribonuclease enzymes so omnipresent? Is this the only reason why RNA is so difficult to work with, or are there other technical hurdles that are more difficult to overcome? Are we missing a big piece of the biological puzzle because of this? Any recent developments in this area?
- keithwhor 6y ago
  RNA is a less stable molecule than DNA — it can be single-stranded, form double strands, self-pair (form loops), react readily with proteins... just difficult to deal with. On top of that, as mentioned, RNAses (enzymes that destroy RNA) are everywhere. Your skin secretes them as an anti-pathogen defense against viral RNA [0]. So do a plethora of other living organisms including single-celled bacteria ubiquitous in the atmosphere and on surfaces. I haven’t heard of any recent developments — it’s been a decade since I was in grad school and now I build software — but I briefly studied a subcategory of ribozyme called self-splicing group I introns which is where my interest comes from. [0] https://en.m.wikipedia.org/wiki/Ribonuclease https://en.m.wikipedia.org/wiki/Ribonuclease [1] https://en.m.wikipedia.org/wiki/Group_I_catalytic_intron https://en.m.wikipedia.org/wiki/Group_I_catalytic_intron
  - jiggawatts 6y ago
    > In addition, active RNA degradation systems are a first defense against RNA viruses, and provide the underlying machinery for more advanced cellular immune strategies such as RNAi. Huh... today I learned. I didn't realise we have such "low-level" immune defences, I always just assumed that the simplest defence we had were antibodies.

keithwhor 6y ago

In a sense we are RNA-based lifeforms. Our protein synthesis machinery is dependent entirely upon RNA. I think there’s a perspective here that the RNA world never disappeared, just became symbiotic with higher-order protein structures. On one hand, RNA viruses continue to replicate successfully (i.e. SARS-nCoV-2) and on the other we rely on rRNA, tRNA and mRNA to function as a highly-conserved part of cellular function across all organisms. When I was in grad school my default assumption was that ribozymes (catalytic RNA) are far more abundant than we currently know. RNA just very difficult to work with so there’s a selection bias against our ability to measure its behavior in vivo.

wombatmobile 6y ago
> In a sense we are RNA-based lifeforms. Our protein synthesis machinery is dependent entirely upon RNA. Yes, we are RNA organisms that have been incorporated into larger organisms, just as we are prokaryotes that have been incorporated into eukaryotes through endosymbiosis. https://evolution.berkeley.edu/evolibrary/article/_0_0/endosymbiosis_04 https://evolution.berkeley.edu/evolibrary/article/_0_0/endos...
- keithwhor 6y ago
  Absolutely the comparison I was intending to convey! Biology is a messy and beautiful place filled with competition and cooperation. :) As much as 8% of our DNA was laterally transferred from viruses! In a sense, some infections result in a symbiosis with a host. https://en.m.wikipedia.org/wiki/Endogenous_retrovirus https://en.m.wikipedia.org/wiki/Endogenous_retrovirus
  - wombatmobile 6y ago
    Lateral DNA transfer is awesome. Check out this visualisation of the molecular apparatus assembled on the surface of a bacterium to inject a chunk of DNA into a neighbouring bacterium. Type 4 secretion system: ii- Pilus biogenesis https://www.youtube.com/watch?v=ihlFqOK5cZM https://www.youtube.com/watch?v=ihlFqOK5cZM
- 6y ago

adrian_b 6y ago

A part of the hypothesis about the RNA world is correct, but all of it seems very unlikely. It is almost certain that DNA appeared later than RNA, probably in some kind of virus. Also, it is a logical necessity that the transcription of RNA into proteins, including the ribosomes and the transfer RNAs appeared only later than the replication of RNA. The part of the RNA world hypothesis that seems unlikely because it has very few supporting data is that the original biocatalysts a.k.a. enzymes were RNA molecules unlike anything that exists today. In my opinion, it is far more likely that the first enzymes were non-ribosomal peptides, somewhat resembling to parts of the proteins that constitute the enzymes of recent life forms. ATP and other nucleotides must have existed before RNA as a means to perform condensation (i.e. dehydration) reactions and the copolymerization of the nucleotides must have appeared as some undesirable side reaction, which somehow at some point generated some sort of self-replicating RNA, which was in fact the first virus, because its synthesis could not have any beneficial effects for the hosting life form. Only after the appearance of the transcription of RNA to proteins, the RNA could evolve into a source of components for the hosting life form so that RNA could change from a parasitic entity to an essential part. Life forms with RNA (and later with DNA) are analog with microprogrammable processors, because the nucleic acid molecules are memories which direct the synthesis of other components, so you can change the components by writing a different information in the memories, without changing the synthesis machinery. This kind of flexibility was certainly necessary for further evolution. Life forms before RNA are analog to hard-coded processors. Supposing that they were made with non-ribosomal peptides, there must have been a mechanism by which a complete life form was replicated, by a cycle of reactions were some kinds of peptides were assembled by other kinds of peptides. Non-ribosomal peptides exist even today in all living beings and they are assembled in the correct sequence from amino-acids without depending directly on the information stored in nucleic acids, like the proteins. Memories, like nucleic acids, are certainly not necessary for designing an ensemble of molecules able of self-replication, exactly like a memory is not necessary for implementing the control automaton of a processor. Nevertheless, it is likely that the further evolution of such a primordial life form was almost impossible, because all accidental changes in the structure of the component molecules would have resulted in a replication failure. After the separation of functions between a memory (nucleic acid) and a generic synthesis machine, evolution by changing the memory content became much more likely to be successful.

pfdietz 6y ago

A problem with RNA world is that RNA, and even ribose, is not very stable. It's not very plausible that the components of RNA could be present in pure forms that could allow faithful RNA replication, even ignoring energy needed for that.

est31 6y ago
RNA viruses do exist. After a certain length, the instability issues you point out cause problems, so usually they have a shorter genome. But I'd say that earliest life forms had shorter genomes anyways. Also, not every copy has to work out. You can see that with viruses, there are viruses where errors in manufacturing render most created viruses inactive.
- pfdietz 6y ago
  RNA viruses exist. They exploit the highly "artificial" conditions inside living cells, where these unstable components are constantly being constructed and undesirable chemicals excluded. A primordial soup, without the precision enzymes and constant energy expenditure of this synthetic machinery, will be a grab bag of random glop. In Miller-Urey experiments the concentrations of any particular chemical decline exponentially with the number of atoms in that chemical. I believe ribose has never been seen in any such experiment (and certainly not in any but extremely low concentration), never mind the triphosphorylated nucleotides that provide the energy to drive RNA synthesis.