The ID Report

By Robert Deyes

John Heilbron's and William Bynum's article '1902 and all that' provided a selection of some of the most prominent discoveries in science over the last few hundred years (Ref 1). To name but a few, Heilbron and Bynum presented Tyco Brahe's accurate positioning of 777 stars in 1602 and Thomas Bartholin's 1652 description of the human lymphatic system (Ref 1). They likewise expounded on Edward Sabine's 1852 discovery of a link between the occurrence of sunspots and variations in the earth's magnetic field as well as Louis Pasteur's announcement of an Anthrax vaccine in 1881. Conspicuous within Heilbron's and Bynum's listing was Stanley Miller's and Harold Urey's 1952 spark discharge experiment which they claimed represented a pioneering achievement in our understanding of the origins of life (Ref 1). What they failed to mention was that this and subsequent prebiotic simulation experiments brought forward too many fundamental (and sometimes unreasonable) expectations about the conditions that would have been prevalent in the early earth (Ref 2). A number of destructive forces and diluting interactions would have decimated the overall concentration of life's building blocks on our earth 3.9 billion years ago (Ref 2).

Of course we have no way of knowing with absolute certainty what the relative frequencies of chemicals, necessary for the biosynthesis of amino-acids, would have been in a hypothetical prebiotic soup since no one was there to see it. To adopt The Economist science editor Geoffrey Carr's catch phrase, what we are dealing with here is "a mountain of theory built on a molehill of evidence" (Ref 3). Nevertheless based on our current knowledge of chemistry we should assume the worst- a disordered, dilute gemish rather than an ordered reaction chamber of purified components and isolated ingredients (Ref 2).

At the end of 2002, two prominent researchers from the Scripps Research Institute, John Reader and Gerald Joyce, took prebiotic chemistry one stage further by generating an RNA 'enzyme'- a Ribozyme- that used only two bases rather than the four we see in DNA today (Ref 4). This was heralded as a major breakthrough in prebiotic chemistry experimentation since, for the first time, there was some indication that early life could have begun using a much simpler genetic code- one made up of only two subunits. Reader and Joyce published their work in Nature at the end of 2002 describing in detail how their so-called 'binary ribozyme' had been generated through successive rounds of in vitro evolution. Such a selective process eventually resulted in efficient catalysts with activities akin to those of cellular enzymes called polymerases (Ref 4).

Parallels were immediately drawn between Reader's and Joyce's experiments and Darwinian natural selection. Since the single cell itself is home to a host of metabolic processes life, according to Reader and Joyce, must have begun in a much simpler form from which it subsequently evolved (Ref 4). The binary code ribozyme thus appeared to present one possible model for explaining how early life may have at one time existed. Needless to say their results did not confirm that a binary genetic code had ever existed. Reader and Joyce themselves stressed that their study did not prove life had started this way (Ref 4). Investigator involvement was clearly influential in assuring the success of the experiment. As with prebiotic simulations the specific components were isolated from other ingredients that would have been present in the 'gemish' of a theoretical prebiotic soup. Here too, destructive processes would have played a fundamental role in diluting out the components of a potentially emerging binary code. The fallacy of the claim that a Darwinian parallel was operational in these experiments was all too obvious when one recalls that natural selection, by its very nature, defines a process based on random mutations that lacks any purpose and direction. Reader and Joyce on the other hand perfected their design as they sought to achieve their 'efficient ribozyme', carefully directing and orchestrating their reactions in the process (Ref 4).

One review of evolutionary biology debates noted how theories on life's origins assume so much while at the same time demonstrating so little about how naturalistic processes could have lead to the first cell (Ref 5). The text book 'Molecular Biology Of The Cell', that is today used by many scientists in the fields of biochemistry, molecular biology and cell biology, added a mountain of speculation to the origin of life debate by proposing that complex biochemical pathways in living cells arose through the successive addition of steps in a reverse order with the final steps of a given pathway appearing first in the evolutionary scheme (Ref 6). For those that accept such a view, the challenge is clear- there is no reason to think that the chemical intermediates would necessarily be available in a hypothetical prebiotic soup simply floating around for gradual incorporation into the early cell's biochemical pathways (Ref 7, p.152). Vital cellular processes such as protein synthesis likewise challenge the concept of a gradual piece-meal assembly of the cell, revealing instead integrated components that must work together to achieve their end function (Ref 8, pp.856-864; pp.896-930). Indeed genes use a genetic code made up of triplet codons- sequences of three bases long in the DNA- that specify which amino acids will get incorporated into a protein during translation (Ref 8, p.900).

The bases in the coding DNA and the amino acids that make up the protein never 'see each other' but are indirectly linked by the message, the messenger RNA, which presents a copy of the code to the translation machinery (Ref 8, pp.924-926). A critical problem arises in the Darwinian model when one considers that gradually altering the genetic code to provide the full complement of amino acid coding triplets would most likely be lethal to any organism simply because such alterations would impact the very proteins that make up the translation machinery. In the words of physicist Paul Davies,

"a change in the code risks feeding back into the very translation machinery that implements it, leading to a catastrophic feedback of errors that would wreck the whole process. To have accurate translation, the cell must first translate accurately". (Ref 9)

Carl Woese has proposed that the amino acid assignments of the genetic code and that the translation mechanisms somehow evolved together (Ref 9). According to Woese, early cells could make do with a sloppy, translation system that lacked fidelity (Ref 9). Yet it seems that a mechanism that faithlessly introduced new amino acids into its own manufacturing process would be much more likely to spiral into a negative feedback loop of destruction than generate any functional improvements. In their discussions on robustness and complexity, J.M Carlson and John Doyle wrote as much

"The simplest bacteria have hundreds of genes. Much simpler CPUs, computers, networks, jets, and cars can be and have been built. What is lost in these simpler systems is not their basic functionality but their robustness. By robustness, we mean the maintenance of some desired system characteristics despite fluctuations in the behavior of its component parts or its environment" (Ref 10).

In other words, hypothetical, precursor translation mechanisms such as those suggested by Woese would be more likely to suffer from fluctuations in the behavior of their component parts than complex, refined machines. Such a lack of robustness clearly argues against Woese's theory of an initial sloppy evolution. Today we know that the translation machinery of the eukaryotic cell is as elegant as it is complex. Indeed one review noted the following machine-like qualities of the ribosome and its ability to correct for errors in translation:

"During the translation of genes to proteins, molecules known as transfer RNAs or tRNAs dock along another RNA molecule, an mRNA, within the ribosome and deliver an amino acid building block to a growing protein. The mRNA codes for each amino acid using a unique codon: a sequence of three adjacent nucleotides in the genetic code....millions of interactions allow an amino acid to navigate into place during the protein-building process....the tRNA has an extra hinge where it holds the amino acid. There also appears to be a special loop in the ribosome through which the end of the tRNA must writhe. If the tRNA codon is misaligned with the mRNA-say, if only two of three RNA bits are correctly matched-the tRNA might hit this loop as it passes" (Ref 11).

A hypothetical cellular translation mechanism that translated inaccurately would lead to a catastrophic loss of functionality. Looking back at Heilbron's and Bynum's list of the historical achievements of science we would do well to reconsider what we truly do know about the origin and evolution of life. As with transcription and translation, contemporary science is revealing precision design in the cellular 'goings on' that defies a naturalistic explanation (Ref 7). More than anybody, those that have contributed to the scientific evidence undergirding the intelligent design movement should be heralded as the great scientists of our day.

References

1. J.L. Heilbron and W.F. Bynum (2002), 1902 and all that, Nature, Vol. 415, pp. 15 -18

2. Charles B Thaxton, Walter L Bradley Roger L Olsen (1984), The Mystery of Life's Origin, Reassessing Current Theories, 2nd Edition, Published by Lewis and Stanley, Dallas, Texas, pp.42-67

3. Geoffrey Carr (2002), The Myth-Makers, The Economist, January 5th, 2002, pp 51-62

4. John S. Reader and Gerald F. Joyce (2002), A ribozyme composed of only two different nucleotides, Nature Vol 420, 841-844

5. Richard Robinson (2005), Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks, PLoS Biol 3(11): e396

6. Bruce Alberts, Dennis Bray, Julian Lewis Martin Raff, Keith Roberts, James D Watson (1989), Chapter 1 of Molecular Biology of the Cell, Published by Garland Publishing Inc, New York, 2nd Ed, pp. 11-12

7. Michael J Behe (1996), Darwin's Black Box-The Biochemical Challenges to Evolution, 1st Edition Published by Simon and Schuster, New York

8. Donald and Judith Voet (1990), Biochemistry, Published by Wiley, New York

9. Paul Davies (1999), The Fifth Miracle The Search for the Origin and The Meaning of Life, Published by Simon and Schuster, New York, p.111

10. J. M. Carlson and John Doyle (2002), Complexity and Robustness, Proc. Natl. Acad.Sci. USA, Vol. 99, Suppl. 1, pp. 2538-2545

11. Eli Kintisch (2005), Tracing tRNA's Tricky Tango, Science 27 October 2005, see paper at http://sciencenow.sciencemag.org/cgi/content/full/2005/1027/2