More marvellous machinery: ‘DNA scrunching’
by Jonathan Sarfati
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 blueprint—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
(1902–1992), 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.
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.7–9
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
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 …
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.
Related articles
Further reading
Recommended Resources
References
- Sarfati, J., Design in living organisms
(motors), Journal of Creation 12(1):3–5, 1998,
<www.creation.com/motor>. Return to text.
- Sarfati, J., DNA: marvellous messages
or mostly mess? Creation 25(2):26–31, 2003;
<www.creation.com/message>. Return to text.
- 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.
- PhysOrg.com,
Nanotech tools yield DNA transcription breakthrough, 16 November 2006.
Return to text.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
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