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There is no biochemical constraint of any sort, so why doesn't some other code work? Why is it specifically RNA/DNA?

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    $\begingroup$ possible duplicate of Why did abiogenesis only happen once? $\endgroup$ – szulat Aug 26 '15 at 23:48
  • $\begingroup$ You are asking two relatively different questions in your post. I'd suggest to restrict your post to only one (and expand on it). $\endgroup$ – Remi.b Aug 27 '15 at 0:57
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    $\begingroup$ I don't think it is a duplicate of "Why did abiogenesis only happen once?". The question above might be reformulated as: "Why hasn't any lineage evolve to use a different genetic code than the ancestor (or than the other lineages)". $\endgroup$ – Remi.b Aug 27 '15 at 0:57
  • $\begingroup$ "If it ain't broke don't fix it?" If there were organisms that used other genetic codes then it would seem they are now extinct; species that used this code had the most progeny surviving to reproduce. New, random mutations that modify some aspect of the translational apparatus, and that would yield a slightly different code, are presumably lethal. $\endgroup$ – mdperry Aug 27 '15 at 10:31
  • $\begingroup$ There is an interesting biochemical question underlying this question: "Why are nucleic acids better than other polymers for our genetic code?" That's what I've answered anyway! $\endgroup$ – James Aug 27 '15 at 10:53
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Preamble

Any answer regarding the origins of our biochemical evolutionary origin will be reasonably speculative given that this is a very hard question to scientifically test and this field is generally understudied to say it is pretty much the most fundamental biochemical question. But there are a few reasons why RNA makes sense as the prime genetic molecule compared to other established macromolecules present in the primordial soup, and also there are good reasons why DNA superseded it as genetic storage for most cellular organisms.

In summary, the alternative abundant polymer macromolecules that came from the primordial soup aren't as versatile as RNA, and over time DNA was used more over RNA due to it being a more reliable information storage molecule.

We must remember though that the conditions that lead to the genesis of RNA is a much tougher question. There are an unfathomable amount of combinations of chemicals that could have facilitated an evolutionary process. @WYSIWYG made an excellent comment regarding why this is an almost impossible question to answer definitively:

...Why is there a phosphodiester backbone used rather than ether, amide, carboxyl ester or any other kind of linkage? Or why purines and pyrimidines, why not naphthalene ring heterocycles? Why imidazole, why not oxazole or furan? You cannot reason this out in a reverse manner.

Therefor in this answer we will be discussing RNA and other bio-polymers that were established in abundance from the very early primordial soup, not the original genesis of such biochemicals. What made each of them good vessels for an evolutionary process?

A genetic code macromolecule needs the following features:

  • Stable.
  • Variable structure.
  • Expandable.
  • Replicable.

RNA has all these and doesn't rely on a biological system for reproduction of the RNA molecule.

RNA world.

Let's not forget that DNA is probably not the first one along and there was an RNA world before the cell as we know it. Even today many viruses particularly make use of ssRNA.

RNA was a good molecule because it was a polymer made of 4 base monomers that could bind with other polymers to make any array of compositions of the base components and was spontaneously replicable. This allowed a primordial form of molecular evolution as we know it today. It is able to carry more varied information than other abundant macromolecule polymers.

RNA can also carry out functions in a similar way a protein might, including catalysis. No known sugars or other macromolecules are able to demonstrate the same level of variability and versatility as RNA, although deoxyribosymes have been artificially designed in laboratories.

This probably gave it a good chance at establishing itself as the first molecule to trigger biogenesis, and this lead to nucleic acids being established as the fundamental molecule of molecular evolution.

enter image description here

DNA chemical structure.

Eventually RNA evolved into more complex structures and DNA broadly superseded RNA as a storage device for genetic information in cellular organisms primarily due to the increased stability DNA offers over RNA. If we take a look at DNA specifically we see a very good data storage mechanism for a couple of reasons.

  1. Intra-strand hydrogen bonding and different chemically structured sugar group makes a more stable overall structure.
  2. More rigid grooves allow proteins to bind at particular sites.
  3. Again, it's a polymer of variable composition.

enter image description here

Alternative coding macromolecules.

What are our other options from the biological polymers?

  • Carbohydrates. The glycocalyx coats most cells in our body, and clearly sugars (specifically polysaccharides and glycoproteins) are an expandable, information rich molecule. However it relies on proteins for assembly in the same way proteins do, so it never really got the chance to be that prime molecule.
  • Lipids. A brilliant expandable polymer, and many are spontaneously expanding in the right conditions, but generally lipids cannot carry as much "information" in the polymer (pretty much just varying lengths of CH2 groups).
  • Proteins. Too complex and not spontaneously replicable. They rely on other systems for production (except in some rare examples, although they arguably still rely on a complex biological system).
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  • $\begingroup$ There can be infinite comparisons. Why take only lipids and proteins for comparison. I can ask why phosphodiester bond as a backbone and not ether, amide, carboxyl ester or any other kind of linkage. Or why purines and pyrimidines, why not naphthalene ring heterocycles. Why imidazole, why not oxazole or furan.. You cannot reason this out in a reverse manner. $\endgroup$ – WYSIWYG Aug 27 '15 at 13:40
  • $\begingroup$ @WYSIWYG excellent point. I think we are talking about different things though, and my answer isn't clear enough. You're talking about the genesis of the primordial soup, I'm describing how RNA was a better vessel for evolution given other established bio molecules. I will edit later to tidy up this point. $\endgroup$ – James Aug 27 '15 at 13:58
  • $\begingroup$ One of the things that you left off of your list as to why DNA is more stable is the 2'-hydroxyl of ribose is reactive and can induce strand breaks where the 2'-hydride of deoxyribose is not a center of reactivity. RNA degrades more rapidly than DNA simply because of the chemical structure of the sugar it is made from. $\endgroup$ – AMR Sep 1 '15 at 2:08
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That is an evidence that all the creatures share a same ancestor from evolution. About the origin of the genetic code, scientists proposed some hypotheses to explain it.

  1. Chemical principles: From the experiments, scientists found that some amino acid have a selective affinity to certain triplet codons.

  2. Biosynthetic expansion: The original creatures may produce amino acids as by-products of metabolism, and then some of these function into the genetic coding. Evidences show that fewer different amino acids were used in the past than today.

  3. Natural selection: The goal of the genetic coding is to minimize the mutation. Some scientists assume that ancient life may have longer codon than triplet codon, such as quadruplet codon, but quadruplet codon have more error that triplet codon, and then only the triplet codon can survive.

  4. Information channel: This hypothesis suppose that the process of genetic code translation is an error-prone information channel. The organisms wanted to inherent their genetic information accurately and efficiently and stay away from the genetic noise. Genetic code should be influenced by three evolutionary force: the needs for diverse amino acids, for error tolerance and for minimal cost of resource. Finally, the genetic coding amino acids become nonrandom.
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  • $\begingroup$ I'm not sure how this answers the question of DNA and RNA being used to carry our genetic information. You're describing general theories about ribosomal translation. I think point 4 might be on point, but even in that point I don't quite understand what you are getting at entirely. $\endgroup$ – James Aug 30 '15 at 17:09
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The interesting thing about evolution is that Mother Nature does not go back to the drawing board and start with a completely new design. Evolutionary changes happen in tiny increments. Faced with a problem like the appearance of oxygen in the atmosphere, evolution did not redo the whole genetic structure of plants. It tinkers. So we ended up with a wasteful and inefficient system. But it works.This kid does the most wonderful humorous video explaining this. Just google Rubisco tubes.

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