More marvellous machinery: ‘DNA scrunching’


Some of the most startling discoveries in the last few decades have improved our understanding of the amazing complexity of the cell. This includes the world’s tiniest machines.1 But not only are there machines, but also their recipe book—the message molecule DNA.2 DNA’s function is to store and transmit genetic information, but it can’t work without many molecular machines. However, as the noted philosopher of science, Sir Karl Popper (1902–1994), commented:

‘What makes the origin of life and of the genetic code a disturbing riddle is this: the genetic code is without any biological function unless it is translated; that is, unless it leads to the synthesis of the proteins whose structure is laid down by the code. But … the machinery by which the cell (at least the non-primitive cell, which is the only one we know) translates the code consists of at least fifty macromolecular components which are themselves coded in the DNA. Thus the code can not be translated except by using certain products of its translation. This constitutes a baffling circle; a really vicious circle, it seems, for any attempt to form a model or theory of the genesis of the genetic code.
The ‘scrunching’ model for RNAP
Figure 1. The ‘scrunching’ model for RNAP–active-centre translocation during abortive initial transcription.5,6
‘Thus we may be faced with the possibility that the origin of life (like the origin of physics) becomes an impenetrable barrier to science, and a residue to all attempts to reduce biology to chemistry and physics.’3

Transcription tricks

Now Richard H. Ebright and his team from Rutgers University have discovered more intricacies in the process of transcription,4 where information from the right part of the DNA is copied onto a strand of messenger RNA (mRNA).5,6 Indeed, it is this mRNA that is translated into proteins in the complex machines known as ribosomes.79

DNA is double stranded, so must first be unwound, so that the right strand can be copied onto mRNA, in a sense like a photographic negative. So the machine, called RNA polymerase (RNAP), first locks on to the start of the gene. Ebright and colleagues demonstrated what happens next with two complementary techniques, single-molecule fluorescence resonance energy transfer (FRET)6 and single-molecule DNA nanomanipulation,5 and were able to rule out other ideas of how it works.

The next stage is that the anchored RNAP then reels in the DNA—scrunching (figure 1).10 This unwinds the double strand so the messenger RNA copy can be formed off one of them. Also, the unwinding stores energy, just like winding the rubber band of a rubber-band-powered airplane. And just like the toy plane, this energy is eventually released, with the machine then breaking free of its starting point and shooting forward. This also rewinds the unwound DNA (‘unscrunching’) which escapes from the back of the machine.

Ebright states that this research should also enable them to develop antibacterial agents that target the bacterial version of this machine.4

Evolutionary conundrum

This discovery provides yet more support for Popper’s bafflement. The instructions to build RNAP are themselves encoded in the DNA. But the DNA could not be transcribed into the mRNA without the elaborate machinery of RNAP. And this is also an example of irreducible complexity because it would not be able to perform its function unless every feature was working fully. There would be no use being able to dock onto the right spot of the gene and getting stuck there, or unwinding the DNA without being able to wind it back.

Furthermore, RNAP uses ATP as an energy source to achieve its feats. And ATP is made by another nano-machine, the ATPase complex, which is a rotary motor.1 This is also coded on the cell’s DNA.

Natural selection is no answer, because this means differential reproduction, i.e. fully formed self-reproducing entities that can pass on the information that codes for their features. But until RNAP is fully formed, the coding would not work at all, being unable to get past first base (pun intended). Thus Darwinian evolution could not even have got off the starting block.

Posted on homepage: 16 October 2008


  1. Sarfati, J., Design in living organisms (motors), Journal of Creation 12(1):3–5, 1998, <creation.com/motor>. Return to text.
  2. Sarfati, J., DNA: marvellous messages or mostly mess? Creation 25(2):26–31, 2003; <creation.com/message>. Return to text.
  3. Popper, K.R., ‘Scientific reduction and the essential incompleteness of all science’; in Ayala, F. and Dobzhansky, T., (Eds.)., Studies in the Philosophy of Biology, University of California Press, Berkeley, p. 270, 1974. We now know that there are many more than 50 ‘macromolecular components’ necessary. Return to text.
  4. PhysOrg.com, Nanotech tools yield DNA transcription breakthrough, 16 November 2006. Return to text.
  5. Revyakin, A., Liu, C., Ebright, R.H. and Strick T.R., Abortive initiation and productive initiation by RNA Polymerase involve DNA scrunching, Science 314(5802):1139–1143, 17 November 2006. Return to text.
  6. Kapanidis, A.N., Margeat, E., Sam On Ho, Kortkhonjia, E., Weiss, S. and Ebright, R.H., Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism, Science 314(5802):1144–1147, 17 November 2006. Return to text.
  7. In ‘higher’ organisms (eukaryotes), it is necessary to remove non-coding parts called introns and splice the coding parts (exons) together. This requires elaborate machinery called a spliceosome—a scientific paper was entitled, ‘Mechanical devices of the spliceosome: motors, clocks, springs, and things’, (Staley, J.P. and Guthrie, C., Cell 92(3):315–326, 1998). This is assembled on the intron, chops it out at the right place and joins the exons together. This must be in exactly the right direction and place, because it makes a huge difference if the exon is joined even one ‘letter’ off. Return to text.
  8. Andrew Fire and Craig Mello won the 2006 Nobel Prize for Physiology and Medicine for their 1998 discovery of RNA interference, where double-stranded RNA can silence the gene, i.e. block protein synthesis. Many of our genes encode small RNA molecules called microRNAs that contain pieces of the code of other genes. These can form a double-stranded structure with mRNA, stopping its translation into proteins, thus instigating ‘RNA interference’. nobelprize.org/nobel_prizes/medicine/laureates/2006/press.html, 11 December 2006. Return to text.
  9. RNA interference involving micro-RNAs has major implications against dismissing much of our DNA as ‘junk’—see Woodmorappe, J., Junk DNA indicted, Journal of Creation 18(1):27–33, 2004. Return to text.
  10. Roberts, J.W., RNA Polymerase, a scrunching machine, Science 314(5802):1139–1143, 17 November 2006 (comment on refs 5 and 6). Return to text.

Helpful Resources

The Stairway to Life
by Change Laura Tan and Rob Stadler
US $12.00
Soft cover