March 2, 2010 | David F. Coppedge

Origin of Life: Claiming Something for Almost Nothing

Getting life to emerge from nonliving chemicals is either a cinch or the most impossible thing in the universe, depending on whom you ask.  Let’s look at a couple of recent papers that suggest the origin of life was no big deal.
    A press release from the University of Colorado advertised a paper by Michael Yarus and team in PNAS.1  The team, funded by a $415,610 grant from the National Institutes of Health, concocted a “Tiny RNA Molecule With Big Implications for the Origin of Life.”  It’s the smallest ribozyme yet, with only five nucleotides, and it is able to “catalyze a key reaction that would be needed to synthesize proteins.”  Tom Blumenthal, a colleague working with Yarus, said, “Nobody expected an RNA molecule this small and simple to be able to do such a complicated thing as that.”  By implication, this ribozyme could have been a stepping stone on the way to larger and more complex molecules of life.
    Yarus has been a strong proponent of the “RNA World” hypothesis.  The team’s findings argue that RNA enzymes (ribozymes) did not have to be as complex at first to have a function.  He said, “If there exists that kind of mini-catalyst, a ‘sister’ to the one we describe, the world of the replicators would also jump a long step closer and we could really feel we were closing in on the first things on Earth that could undergo Darwinian evolution.”  He refers to the fact that Darwinian evolution by natural selection cannot be invoked till there is a replicator – a system able to duplicate its parts accurately.  Yarus admitted, “the tiny replicator has not been found, and that its existence will be decided by experiments not yet done, perhaps not yet imagined.
    But does this work support a naturalistic origin of life?  A key question is whether the molecule would form under plausible prebiotic conditions.  Here’s how the paper described their work in the lab to get this molecule:

RNA was synthesized by Dharmacon. GUGGC = 5’-GUGGC-30 ; GCCU – 5’P-GCCU-3’ ; 5’OH-GCCU = 5’-GCCU-3’ ; GCCU20dU = 5’-GCC-2’-dU; GCC = 5’-GCC-3’ ; dGdCdCrU = 5’-dGdCdCU-3’ . RNA GCC3’dU was prepared by first synthesizing 5’-O-(4,4’- Dimethoxytrityl)3’-deoxyuridine as follows: 3’-deoxyuridine (MP Biomedicals; 991 mg, 0.434 mmol) was dissolved in 5 mL anhydrous pyridine and pyridine was then removed under vacuum while stirring.  Solid was then redissolved in 2 mL pyridine.  Dimethoxytrityl chloride (170 mg, 0.499 mmol) was dissolved in 12 mL pyridine and slowly added to 3’-deoxyuridine solution.  Solution was stirred at room temperature for 4 h.  All solutions were sequestered from exposure to air throughout.
    Reaction was then quenched by addition of 5 mL methanol, and solvent was removed by rotary evaporation.  Remaining solvent evaporated overnight in a vacuum chamber.  Product was then dissolved in 1 mL acetonitrile and purified through a silica column (acetonitrile elution).  Final product fractions (confirmed through TLC, 1.1 hexane:acetonitrile) were pooled and rotary evaporated.  Yield was 71%. Dimethoxytrityl-protected 30dU was then sent to Dharmacon for immobilization of 30-dU on glass and synthesis of 5’-GCC-3’-dU.
    PheAMP, PheUMP, and MetAMP were synthesized by the method of Berg (25) with modifications and purification as described in ref. 6.  Yield was as follows: PheAMP 85%, PheUMP 67%, and MetAMP 36%.

Even more purification and isolation steps under controlled conditions, using multiple solvents at various temperatures, were needed to prevent cross-reactions.  It is doubtful such complex lab procedures have analogues in nature.  They started with pre-existing ribose, furthermore, and did not state whether it was one-handed.  The putative ribozyme function only consisted of one step of a complex multi-step reaction in living organisms: “The small ribozyme initially trans-phenylalanylates a partially complementary 4-nt RNA selectively at its terminal 2’-ribose hydroxyl using PheAMP, the natural form for activated amino acid.
    The team’s interpretation of the significance of their work relies heavily on imagination: “The ultimate importance of these observations may lie partly in the unknown number of other reactions that can be accelerated by comparably small RNAs.”  They simply assumed that a “geochemical source” would be able to produce a suite of other five-nucleotide ribozymes, including theirs.  “On one hand, with this few ribonucleotides to dispose in space, there may not be other similar nucleotide structures that are both stable and capable of catalysis,” they concluded.  But then they relied on future work and imagination: “On the other hand, for obvious reasons, it will be extraordinarily important to look for other tiny RNA active centers, now knowing they can exist.”  Finally, another reason they worked on the RNA-World hypothesis is that they recognized that “it is implausible that primitive peptides were synthesized using already-formed protein catalysts….”  It must be remembered, too, that these chemical reactions, even if they could occur naturally, have no forward-looking capacity.  They have no desire or power to direct their work toward the goal of producing life.  Because natural selection is out of the question before accurate self-replication, any success will be strictly due to chance.
    A prerequisite for RNA is sugar.  How did they arise?  Another recent paper in Science might be called the rock candy theory for the origin of life.2  The authors argue that sugars might form naturally in the formose reaction and be stabilized in silicates.  They called this a “bottom-up synthesis of sugar silicates.”  Recognizing that previous work on the formose reaction produced mixtures that were complex and unstable, they argued that “Silicate selects for sugars with a specific stereochemistry and sequesters them from rapid decomposition.  Given the abundance of silicate minerals, these observations suggest that formose-like reactions may provide a feasible pathway for the abiotic formation of biologically important sugars, such as ribose.”  For a summary of this paper, see Royal Society of Chemistry (RSC) press release.  The research was supported by the National Science Foundation, Dow Corning Corp. and Schlumberger Ltd.
    The formose reaction “is a possible process whereby sugars form abiotically,” they said.  “This reaction converts formaldehyde (HCHO; C1) to a variety of sugars, in the presence of strong bases, organic bases, or minerals.”  Problem is, it “generates a plethora of unstable sugars, of which the key sugar, ribose, is present in a very small proportion.”  And, “An additional drawback is that the products from the formose mechanism are racemic [mixed-handed], whereas sugars under terrestrial biological conditions are homochiral” (one-handed).  Their work showed that some of these limitations can be overcome with silicates.
    A look through the paper, however, shows complex lab procedures that are hard to justify in nature.  They claimed that “This bottom-up synthesis of sugar silicates is a plausible prebiotic process,” but noted that the sugars “oligomerize very slowly” and “uncomplexed higher sugars decompose rapidly under alkaline conditions.”  The RSC article states, though, that high alkaline conditions are required for the scenario, and that most of the silicates formed in weathering processes are consumed by other reactions.  To delay the decomposition, the sugars have to be complexed quickly on silicates or clays.  But they did not say how complexing the sugars with silicates might prevent, rather than accelerate, downstream biogenetic reactions.  So in their best-case scenario, some sugars might form in the formose reaction, and be sequestered in silicate complexes.  Ribose (essential for RNA) would constitute a tiny fraction of product (see 11/05/2004).
    At some point, something would have had to take the correct sugars out of the silicate cabinet and use them to assemble RNA while preventing damaging cross-reactions occurring with other compounds.  Even then, the problem of sequencing the nucleotides – the key question – has not been addressed.  Where did the genetic code come from?  One ribozyme is not a code.  Unless and until all the ingredients for a self-replicating system are accounted for, none of these suggestive steps constitute progress toward the origin of life.

1.  Turk, Chumachenko and Yarus, “Multiple translational products from a five-nucleotide ribozyme,” Proceedings of the National Academy of Sciences February 22, 2010, doi: 10.1073/pnas.0912895107.
2.  Lambert, Gurusamy-Thangavelu and Ma, “The Silicate-Mediated Formose Reaction: Bottom-Up Synthesis of Sugar Silicates,” Science, 19 February 2010: Vol. 327. no. 5968, pp. 984-986, DOI: 10.1126/science.1182669.

Origin-of-life research suffers from a glaring flaw: lack of critical analysis.  Papers and press releases like this should immediately be subjected to unbiased criticism: “Those are not plausible prebiotic conditions!” or “How would nature sequester the desired compounds from damaging cross-reactions without the techniques you used?”  Many more questions should be asked.  Instead, because secular science has a vested interest in making the origin of life sound simple on the way to Darwinism, the journals allow these views to be aired uncontested.  It presents a false impression that science is making progress toward an answer in little, cumulative steps.  Institutions like the University of Colorado also have a vested interest in making their professors look good in the media.
    If Big Science would do its job, the creationists and intelligent design community would not have to be cast in the role of spoil sports, showing why these ideas won’t work.  They won’t work anyway, but other insiders, not just the expelled, should be saying so.  After all, much of the work was paid for with taxpayer dollars.  Where are the watchdogs?
In the Big Rock Candy Mountains, science takes a holiday;
Your funding comes around once a week and it’s Darwin Day every day.
You never have to clean your lab or put formose away;
There’s a little white lie you can wink your eye,
Notions jump so high they can touch the sky
In the Big Rock Candy Mountains.

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Categories: Origin of Life

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