Origins of Life – Can RNA Spontaneously Assemble?

ResearchBlogging.orgWe know that it is almost trivial for inorganic compounds to spontaneously react to form organic compounds.  We can see this in hundreds, if not thousands of similar experiments since Miller-Urey.  We can also observe these organic products in places that no organic life form could survive; comets and nebula.  So that part is easy.  We can get the precursor materials needed for life to form without invoking anything bu basic chemistry and physics.

So, now the question is, can we get from amino acids, simple sugars, basic nucleic acids and the like to something complicated like RNA?  Can this happen spontaneously, with nothing more than basic physics and chemistry?

The answer, as shown by Matthew W. Powner, Beatrice Gerland & John D. Sutherland, is simply… yes.

First of all, everyone should remember that science will probably never know exactly how life on Earth began.  However, as long as it can be shown that the materials and processes can arise by purely natural means, then there is no need to incorporate a designer or deity to do the job.

Now, on with the research.  First, what’s the big deal?  Why is it so hard to generate X provided that you have V and W?

I’ll let the authors explain:

In particular, although there has been some success demonstrating that ‘activated’ ribonucleotides can polymerize to form RNA [6,7], it is far fromobvious howsuch ribonucleotides could have formed from their constituent parts (ribose and nucleobases). Ribose is difficult to form selectively [8,9], and the addition of nucleobases to ribose is inefficient in the case of purines [10] and does not occur at all in the case of the canonical pyrimidines [11].

In other words, there is evidence that activated ribonucleotides (A, U, C, and G) can form RNA, but the problem is in the sugar and phosphate backbone.  The sugar (ribose) is hard to form and it’s even harder to attach it to some of the nucleobases and it won’t attach to other nucleobases at all.

As my dad would say; “That there is some trouble.”

So, the researchers took a different route.  Instead of starting with the base materials (ribose, the nucleotides, and phosphates), they started to explore alternative chemical paths to get the same result (that is, RNA).

What they found, was that by starting from the exact same precursors that has been shown to be chemically possible, they found another path.  A series of chemical reactions that avoids all the problems of the ‘traditional’ pathway.

Their chemical path simply bypasses ribose and the free pyrimidine nucleobase.  What they also found was that by avoiding trying to incorporate phosphate into the structure directly and, instead, using inorganic phosphate as a catalyst, they were able to increase the yield of the materials they needed at the conditions (pH mainly) that those materials had to have to form.  In fact, having the phosphate present helped increase yields of all intermediate materials.

Finally, in the last step, inorganic phosphate acted as a buffer to prevent an increase in pH that would reduce yields.

I freely admit that I’m not a biochemist (thank Cthulu), but I can understand conclusions very well and considering that this paper appears to be highly cited and generally well received (I do know of one or two hold outs), I think this paper shows what it needs to.  That there is a chemically plausible way to get from inorganic materials all the way to RNAs.

I’ll let the authors’ conclusion speak for itself:

Our findings suggest that the prebiotic synthesis of activated pyrimidine nucleotides should be viewed as predisposed. This predisposition would have allowed the synthesis to operate on the early Earth under geochemical conditions suitable for the assembly sequence.

_________________________________________________

Powner MW, Gerland B, & Sutherland JD (2009). Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature, 459 (7244), 239-42 PMID: 19444213

references (from reviewed paper)

8. Kofoed, J., Reymond, J.-L. & Darbre, T. Prebiotic carbohydrate synthesis: zincproline
catalyzes direct aqueous aldol reactions of a-hydroxy aldehydes and
ketones. Org. Biomol. Chem. 3, 1850–1855 (2005).
9. Ricardo, A., Carrigan, M. A., Olcott, A. N. & Benner, S. A. Borate minerals stabilize
ribose. Science 303, 196 (2004).
10. Fuller, W. D., Sanchez, R. A. & Orgel, L. E. Studies in prebiotic synthesis VI.
Synthesis of purine nucleosides. J. Mol. Biol. 67, 25–33 (1972).
11. Orgel, L. E. Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem.
Mol. Biol. 39, 99–123 (2004).

This entry was posted in Biology, Creationism / ID, Origins of Life, Research Blogging, Science and tagged , . Bookmark the permalink.

22 Responses to Origins of Life – Can RNA Spontaneously Assemble?

  1. Joe G says:

    This is old news.

    Mother Nature is good at making stones, yet it can’t make a structure like Stonehenge.

    Getting the building blocks doesn’t get you the building.

  2. ogremkv says:

    Old news? Really. 2009 is old?

    Whatever.

  3. Rich says:

    “Getting the building blocks doesn’t get you the building.”

    Get you closer than not having them, though.

  4. Joe G says:

    Rich:

    Get you closer than not having them, though.

    Closer to what?

  5. tybee says:

    @JoeG – how can you tell if something is designed or not?

  6. Joe G says:

    @tybee- by investigating and figuring out what it takes to account for whatever it is.

    Forensic science and archaeology do it all the time as do insurance agents.

    The design inference, how it works

  7. ogremkv says:

    OK Joe,

    Since you know how to do it…

    Fantastic. Now, let’s put it to the test. There are two sequences of DNA. Both code for a protein. One is designed (we know because a human designed it). One is not (we know because it has a couple of random changes, that, while remaining functional, are random and of a known non-design).

    Which is which. If ID tools can’t tell the difference, then it’s useless.

    1 taaagatgag tcttctaacc gaggtcgaaa cgtacgttct ttctatcatc ccgtcaggcc
    61 ccctcaaagc cgagatcgcg cagagactgg aaagtgtctt tgcaggaaag aacacagatc
    121 ttgaggctct catggaatgg ctaaagacaa gaccaatctt gtcacctctg actaagggaa
    181 ttttaggatt tgtgttcacg ctcaccgtgc ccagtgagcg aggactgcag cgtagacgct
    241 ttgtccaaaa tgccctaaat gggaatgggg acccgaacaa catggataga gcagttaaac
    301 tatacaagaa gctcaaaaga gaaataacgt tccatggggc caaggaggtg tcactaagct
    361 attcaactgg tgcacttgcc agttgcatgg gcctcatata caacaggatg ggaacagtga
    421 ccacagaagc tgcttttggt ctagtgtgtg ccacttgtga acagattgct gattcacagc
    481 atcggtctca cagacagatg gctactacca ccaatccact aatcaggcat gaaaacagaa
    541 tggtgctggc tagcactacg gcaaaggcta tggaacagat ggctggatcg agtgaacagg
    601 cagcggaggc catggaggtt gctaatcaga ctaggcagat ggtacatgca atgagaacta
    661 ttgggactca tcctagctcc agtgctggtc tgaaagatga ccttcttgaa aatttgcagg
    721 cctaccagaa gcgaatggga gtgcagatgc agcgattcaa gtgatcctct cgtcattgca
    781 gcaaatatca ttgggatctt gcacctgata ttgtggatta ctgatcgtct ttttttcaaa
    841 tgtatttatc gtcgctttaa atacggtttg aaaagagggc cttctacgga aggagtgcct
    901 gagtccatga gggaagaata tcaacaggaa cagcagagtg ctgtggatgt tgacgatggt
    961 cattttgtca acatagagct agagtaa

    1 gaattcggct atgaatctgt ctggtactgg attttcttgg ttggtaggct atcagttact
    61 gcctcagttt cagaacttgt taatggtcta ttcatgaatt taacatcttc ctggtgtaga
    121 catgggaggg tgtatacgtc aaggcattta tccatttctt ttagattatc tagtttattt
    181 gccgagagct gtttatagta ttatctgatg gtagtttcta tttctgtggg atcagtggtg
    241 atattcccta tatcagtttt tgttgcatct attttatttt tctctctttt cttctttatt
    301 attttggcta gtggtctatc tattttgttg atattctcaa aaaaccagcg cgtggattta
    361 ttgatttttg aaagtttttt ttgaactatc tcctttagtt cttctctgat gttagttatt
    421 tcttgtcttc tgctagcttt tgaattggtt tgctgttact tcactatttc ttttcatttt
    481 aatgttagcg tgtctatttt agatctttcc tgctttatct tgtgggcatt taatgctatc
    541 aatttttctc tacacactgc tttaaatgtg ccccagagat ggtgatacgt tgtgtcttca
    601 ttatcattgg tatcaaagaa catctttatt tctgccttat tttgttattt actcatcagt
    661 gatttaggaa caggttgttc aatttctatg ttgttgtgtg gttttgagtg agtttcttaa
    721 tctgggttct aatttgattg cactatggtc tggaaggctc tttgttataa tttgcattct
    781 ttggcatttg ttgaggagtg ttttacttcc aattatgtgg tcaatttttg aatacatgtt
    841 atgtgacacc gagaagaatg tatattctgt tgattggggg tggatagttc tgcagatgtc
    901 tattaggttt acttagtcca cagctgattt caggtcctgc aaatccttgt taattttctg
    961 cctcattgat tgctgcctgt tcttttctct ggaagcttca tccccaaggg

  8. Joe G says:

    Your “test” has nothing to do with ID. It doesn’t have anything to do with science.

    If both code for a protein then both have a specification. Also the design inference is pitted against chance and necessity. And there isn’t any way you can show that eother sequence can arise via chance and necessity.

    But anyway you won’t publish this so it doesn’t matter anyway- you will run around the table with your hands in the air as if you just accomplished something.

    I am saving all my comments and posting links to your cowardice…

  9. ogremkv says:

    As long as you refrain from discourtesy and attempt to discuss in an adult fashion, then I will approve your comments. I will not allow you to insult me or anyone else on my blog. I will continue to allow posts that show you can’t do what you claim to be able to do. I will also allow any comments where you attempt to do what you claim to be able to do.

    As far as you avoiding the test. You said that people can decide on design versus random all the time. Both of the sequences I present code for a protein, the random one has been vetted so that it does not contain a stop codon in the middle, but that’s it. No changes have been made to the sequence. Still one is random and one is not. So design IS being pitted against chance. It’s not my job to tell you that these sequences could arise from chance. That’s not the challenge.

    The challenge is to do the one thing that Intelligent Design proponents (including you) have claimed that it can do. That is detect design. If ID cannot detect design, then it is useless.

    Your (and everyone else’s) inability to even attempt to determine which of these is designed and which is random shows that ID is without basis.

  10. Joe G says:

    And unless one of them was produced by randomly selecting nucleotides it has no bearing on ID.

    That means the entire sequence was produced by randomly selecting nucleotides.

  11. tybee says:

    @Joe G – provide the algorithm to decipher design from non-design.

    and provide it here. just to show you really do have one….

  12. ogremkv says:

    Sorry, moderated because of “Joe G”.

    He can’t. He won’t.

  13. Pingback: Origins of Life – Darwin’s Little Warm Pond | Cassandra's Tears

  14. Eugen says:

    Hi Ogre

    above experiment looks just like an exercise in chemical engineering. Those engineers are obviously very good.

  15. ogremkv says:

    hmmm… well, within the realm of chemical engineering that is just putting materials into test tubes and controlling a variety of conditions, then I agree (and I think biochemists would be a little insulted at being called chemical engineers, but I could be wrong).

    If you mean that there was a concerted effort to design a chemical pathway that resulted in the formation of RNAs, then I’d disagree.

    The RNA formed under conditions that were plausible on the prebiotic Earth.
    The paper explains why the conditions that the authors used is plausible. In other words, these chemical reactions happen. When the listed precursors meet under the listed conditions, the chemical reaction happens. There isn’t a designer stepping in and making the reaction happen.

    Which is the point of the paper and my exploration of origins of life research. ID proponents have pretty much been reduced to abiogenesis claims because that’s all that they can come up with that isn’t answered already. These papers show that there is a plausible, non-designed chemical path from inorganic compounds to life.

    I hope that helps.

  16. Eugen says:

    Hi again

    “ID proponents have pretty much been reduced to abiogenesis claims”
    I’m not sure about that.

    Anyway,before I start yapping I ‘ll read that paper .

    Oops just checked ,it’s text-for-cash. I’m not paying 32 bucks.

    I’ll dig online a bit see if there’s more.

  17. ogremkv says:

    Well, if you can find a positive statement of support for intelligent design, you’re doing better than anyone else on the planet. 😉

  18. Eugen says:

    I’m Neo from Matrix. 🙂

    I’m busy now.We’ll see you later,maybe tomorrow.

  19. Ogre: Thanks for posting the challenge. I admit to being curious exactly how you meant it, and now I know.

    Joe Writes: “And unless one of them was produced by randomly selecting nucleotides it has no bearing on ID.
    That means the entire sequence was produced by randomly selecting nucleotides.”

    Seriously? Is that really the test? I’d ask if Joe were kidding, but I think I know the answer. Let’s put this is a different context: If I digitize a book, make a copy, randomly rearrange all the characters in one copy, and purposefully rearrange the characters in the other to tell a different story, can we tell the difference? Sure we can, but we have learned absolutely nothing. What has that got to do with how proteins evolve? Also absolutely nothing. The test is useless for it’s intended purpose, and I’m not sure what purpose could be found for it. This is like putting two copies of War and Peace through a shredder, reassembling one of them, and then running around claiming to be Tolstoy.

    Congratulation to Joe Tolstoy, who can now reliably detect the difference between a book and a pile of shredded paper.

    Let’s try again, and back to nucleotides. If we start with two sequences, randomly swap two letters in one, and purposely swap two letters in the other, can we detect which one is the purposeful designed? No? Good news! There’s is at most a 50% chance of being wrong if we guess.

  20. Eugen says:

    I re read your post and I only see it as well guided bio chemical experiment. Did anybody ever perform an honest experiment by putting 20 amino acids into sterile container, close it and after a year check if there is protein (or few ) self assembled there ?

  21. ogremkv says:

    Check the other Origins of Life post – the Darwin’s Little Warm Pond one. Oh, I reread your comment and no one, I don’t think any scientists would expect amino acids to form polymers without RNA present. Maybe you could look that up and see what you find.

    I’m doing this series (currently) as an RNA World hypothesis.

    Remember Eugen, the object of this is NOT to create a new form of life. The object is to determine if it is biochemically feasible for it to have occured. The results speak for themselves. It is. The DLWP explains a second pathway to long chain RNAs. There are now, at least, two plausible chemical paths from base inorganic materials to long chain RNAs.

    A future post (hopefully later this week) will cover basic replicators.

    So you see, the pieces are there. We don’t need the whole picture from start to finish. It would be cool, but not probably not feasible within a human lifetime.

    I hope that helps.

    Hey Joe, this is how to have a discussion… see how polite everyone is, with asking questions and the like?

  22. Pingback: Origin of Life – RNA Self Replicators | Cassandra's Tears

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