Catalytic RNA An Unworthy Catalyst For A Serious ‘Origins’ Discussion
|November 20, 2009||Posted by Robert Deyes under Intelligent Design|
The search for extra-terrestrial life has been a passionate focal point of space exploration for decades. While the idea of aliens eking out an ‘other-world’ existence continues to fuel scientific and religious debate, most recently with the Pontifical Academy of Sciences’ astrobiology conference (1), a similarly concerted search for life has focused on primitive unicellular organisms (2). Astrobiologist Richard Hoover and others have long advocated the idea that simple life exists outside of our own earth (3-4). Since NASA’s Galileo spacecraft flyby mission to Jupiter’s moon Europa in 1998, there has been no end to discussions over whether or not this ice-bearing moon might today harbor bacteria (5-6).
The notion that life could simply evolve wherever appropriate environmental conditions are to be found is of course one that entails an enormous ‘leap of faith’. It is a notion that pushes aside a multitude of critical factors not least of which is the origin of some sort of information-rich genetic material. As Stephen Mojzsis from the University of Colorado analogized, just because the stage is set in a theater does not mean that the actors are present and ready to play their respective roles (7). What processes would have been operational to take a maelstrom of chemical compounds to the required level of minimal function upon which Darwinian natural selection could get a hold?
Paleontologist Niles Eldredge captured the pertinence of this question in his discourse on evolutionary tempos when he wrote how “there is a tremendous difference between a collection of organic molecules unable to abstract the energy needed to catalyze their own replication and an organized system that can do precisely that” (8). Prominent thinkers such as Paul Davies have made their appeal to chance by espousing the idea that life was able to begin precisely because it ‘managed’ to liberate itself from the shackles of physical laws and the deterministic, algorithmic world (9). Davies argues that for genomes to become as information-rich as they are, life would have had to have originated from random polymers since, according to Davies, an initial randomness is the only way that we could have arrived at specified biological complexity (9). Still, how could chance-generated polymers that lacked any functional and replicative activities have gained such activities purely through random events?
The last twenty years have given us some interesting avenues of research in the field of catalytic RNA. Experiments in the late 1980s and 1990s revealed that certain types of RNA had intrinsic catalytic activities (10). Renowned RNA biochemists such as Tom Cech, Dan Hershlag, Luc Jaeger and Anne Marie Pyle provided key details on how RNA could fold into catalytically active forms (10-12). With the demonstration of its enzyme and information-bearing capabilities, RNA became a hot candidate for the molecule that might have kick started the beginnings of life (13). The message promulgated by supporters of the much-publicized ‘RNA World’ was that through Darwinian natural selection random mutations might have produced catalytic activities that were further improved through successive generations of replication (13).
Perhaps to the disappointment of ‘RNA Worlders’, Duke University chemist David Deamer and others convincingly discredited such a message on the grounds that those processes necessary for the formation of RNA polymers would have been highly inefficient on a lifeless earth. Their conclusions were profound:
“It is now clear that an RNA world (or even its molecular precursor, pre-RNA) would be difficult to achieve directly from simple organic molecules dissolved in a global ocean (Joyce, 1991). Even if it were possible to generate chemically activated nucleotides capable of polymerizing into RNA in solution, in the absence of some concentrating mechanism these would be greatly diluted, and no further reactions could occur…[Such] inherent inefficiencies would seem to be inconsistent with moving beyond the initial stages of generating monomers and perhaps random polymers.” (13)
My own research during my time at the University of Strasbourg served to further strengthen my own skepticism over the role of RNA in biological origins (14). Using RNA folding algorithms, I worked with others to design special catalytic RNAs called ribozymes that would target and cut highly defined mRNA sequences within the cell (See Figure Below; Ref 15). As I soon found out, not only did these molecular ‘scissors’ have to meet strict sequence requirements if they were to discriminate between target and erroneous mRNAs but they also had to be short enough so as to free themselves from their reaction products and become available for further rounds of cutting (16). This latter point is of critical importance if catalytic RNA is to exhibit what enzymologists call ‘multiple turnover’ behavior- that is, the ability to repeatedly catalyze a given reaction (17).
One could hardly claim that my meticulous crafting of RNA into functional catalysts paralleled the Darwinian process of selection. Had I not chosen my sequences carefully I would not have obtained the desired effects when I introduced these RNAs into the cell. My own findings echoed the sentiments of protein structuralist Thomas Creighton who commented how “the primary difficulty with the scenario of the RNA world is that it is difficult to explain how RNA molecules could have been synthesized chemically in the primordial soup” (18).
While several types of activity have now been identified in synthetic ribozymes including peptide bond formation and RNA ligation, the range of such activities pales in comparison to the extensive repertoire of known protein functions (19). To what extent can we therefore consider catalytic RNA to be sufficient for the formation of components that might later assemble into the simplest forms of life? Moreover, achieving such activities in the laboratory is only possible through the directed guidance of random RNA molecules towards pre-determined functional end points (19, 20).
Writing in the 1970’s, Richard Dawkins cooked up the following ‘requiem to naturalistic causation':
“[The Primeval Soup] must have become populated by stable varieties of molecules; stable in that either the individual molecules lasted a long time, or they replicated rapidly, or they replicated accurately. Evolutionary trends toward these three kinds of stability took place in the following sense: if you had sampled the soup at two different times, the later sample would have contained a higher proportion of varieties with high longevity/fecundity/copying-fidelity. This is essentially what a biologist means by evolution when he is speaking of living creatures, and the mechanism is the same- natural selection.” (21)
Thirty years on we still have no meat on the bones of Dawkins’ dreamy peregrinations. From an RNA World perspective at least I remain thoroughly unconvinced.
1. Tom Chivers (2009) The Vatican Joins The Search For Alien Life, See http://www.telegraph.co.uk/science/space/6536400/The-Vatican-joins-the-search-for-alien-life.html
2. David Malin (2004) Heaven and Earth: Unseen by the Naked Eye, Phaidon Press, UK 2004, p.284
3. Kate Tobin (2009) Extremophile Hunter: The search is on for extremophiles that may provide insights about life elsewhere in the cosmos, See http://www.nsf.gov/news/special_reports/science_nation/extremophile.jsp
4. Jeff Hecht (2001), Life will find a way, New Scientist 17th March, 2001, p.4
5. Patrick Barry (2009) A Tale Of Planetary Woe, See http://science.nasa.gov/headlines/y2009/06nov_maven.htm?list207640
6. Clues To Possible Life On Europa May Lie Buried In Antarctic Ice (1998) See http://science.nasa.gov/newhome/headlines/ast05mar98_1.htm
7. Stephen Mojzsis spoke on the origins of life in a NOVA documentary that aired on PBS on the 28th of September 2004, entitled “Origins: How Life Began”
8. Niles Eldredge (1987) Life Pulse: Episodes From The Story of The Fossil Record, Facts On File Publications, New York, p.30
9. Paul Davies (1999) The Fifth Miracle, The Search for the Origin and The Meaning of Life, Simon & Schuster, New York, pp.250-257
10. T. R. Cech and D. Herschlag (1997) Group I Ribozymes: Substrate Recognition, Catalytic Strategies and Comparative Mechanistic Analysis, Nucleic Acids and Molecular Biology, Vol 10 pp. 1-17
11. L. Jaeger, F. Mitchel, E. Westhof (1997) The Structure Of Group I Ribozymes, Nucleic Acids and Molecular Biology, Vol 10 pp.33-51
12. A.M. Pyle (1997) Catalytic Reaction Mechanisms and Structural Features of Group II Intron Ribozymes, Nucleic Acids and Molecular Biology, Vol 10 pp.75-107
13. David Deamer, Jason Dworkin, Scott Sandford, Max Bernstein, Louis Allamandola (2002) The First Cell Membranes, Astrobiology, Vol 2 pp.371-381
14. Robert Deyes (1998) Unpublished observations, Work done at LPCCNM-UPRES 2308, Faculte De Pharmacie, Universite Louis Pasteur, Illkirch, France
15. Michael Zuker (2003) Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res, Vol 31 pp.3406-15 (this is updated from the version I used in my research)
16. Daniel Herschlag (1991) Implications Of Ribozyme Kinetics For Targeting The Cleavage Of Specific RNA Molecules In Vivo : More Isn’t Always Better, Proc. Natl, Acad, Sci. USA , Vol 88 pp. 6921-6925
17. Thomas Creighton (1993) Proteins, Structure and Molecular Properties, W.H. Freeman and Company, New York, p.387
18. Ibid, p.107
19. Michael P. Robertson and William G. Scott (2007) The Structural Basis of Ribozyme-Catalyzed RNA Assembly, Science, Vol. 315 pp.1549-1553
20. Gordon C. Mills and Dean Kenyon (1996) The RNA World: A Critique, Origins & Design 17:1, See http://www.arn.org/docs/odesign/od171/rnaworld171.htm#note4
21. Richard Dawkins (1989) The Selfish Gene, 2nd Ed, Oxford University Press, Oxford, UK, p.18