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New DNA repair enzyme discovered

Published: 13 January 2011 (GMT+10)
alkD Repair Enzyme
Figure 1: Bacillus cereus alkylpurine DNA glycosylase alkD bound to DNA containing a G-T mismatch.

(www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=84991)

by

Our information is stored on the famous DNA double helix molecule. This is so efficient that just five round pinheads full of DNA could hold all the information of the earth’s entire human population.1 Just one of these pinheads would have 2 million times the information content of a 2 TB hard drive. And each of our 100 trillion cells has 3 billion DNA ‘letters’ (called nucleobases) worth of information.2

But chemically, DNA is actually a very reactive molecule (and RNA is even more so), so it’s highly implausible that it could have arisen in a hypothetical primordial soup.3 Indeed, about a million DNA ‘letters’4 are damaged in a cell on a good day. One common form of DNA damage is called alkylation—this means a small hydrocarbon group is attached to one of the ‘letters’, and there are many places for the attachment. This changes the shape enough so it can no longer fit into the double helix. This can prevent DNA replication or reading the gene.

So living creatures must have elaborate DNA repair machinery. University of Chicago biologist James Shapiro points out that:

all cells from bacteria to man possess a truly astonishing array of repair systems which serve to remove accidental and stochastic sources of mutation. Multiple levels of proofreading mechanisms recognize and remove errors that inevitably occur during DNA replication. … cells protect themselves against precisely the kinds of accidental genetic change that, according to conventional theory, are the sources of evolutionary variability. By virtue of their proofreading and repair systems, living cells are not passive victims of the random forces of chemistry and physics. They devote large resources to suppressing random genetic variation and have the capacity to set the level of background localized mutability by adjusting the activity of their repair systems.5

For example, there is ‘base excision repair’: special enzymes called DNA glycosylases run down the DNA molecule, detect the damaged ‘letter’, grab it, put it in a specially shaped pocket, then chop it out. Then other enzymes repair the resulting gap.

Natural selection requires that the information selected for can be reproduced accurately. But without an already functioning repair mechanism, the information would be degraded quickly.

Scientists at North American universities have discovered another ingenious repair enzyme in bacteria, called AlkD.6 This has a very different structure. It works by flipping a positively charged damaged base—highly unstable—and the one it’s paired with, from the inside to the outside of the helix. Then they are both detached, and the gap filled. Understanding these enzymes could lead to more effective chemotherapy.

Evolution has a major problem in explaining repair machinery. Natural selection requires that the information selected for can be reproduced accurately. But without an already functioning repair mechanism, the information would be degraded quickly. Furthermore, the instructions to build this repair machinery is encoded on the very molecule it repairs, another vicious circle for evolution.7

There is seemingly no end to the machinery required even for the first “simple” cell to evolve. See the related articles as well as following clips from our YouTube channel, CreationClips:

The 20-nanometer motor (height), ATP synthase (one nanometer is one thousand-millionth of a metre). These rotary motors in the membranes of mitochondria (the cell’s power houses) turn in response to proton flow (a positive electric current). Rotation of the motor converts ADP molecules plus phosphate into the cell’s fuel, ATP.

Kinesin is the miniscule longshoreman (stevedore) of the cell, toting parcels of cargo on its shoulders as it steps along a scaffolding of microtubules. Each molecule of ATP fuel that kinesin encounters triggers precisely one 8-nanometer step of the ‘longshoreman’.
See www.umich.edu/news/MT/04/Fall04/story.html?molecular.



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Further Reading

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References

  1. Gitt, W., Dazzling Design in Miniature, Creation 20(1):6, 1997. 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. According to Brooks, J., and Shaw, G., Origins and Development of Living Systems, Academic Press, London and New York, 1973: “If there ever was a primitive soup, then we would expect to find at least somewhere on this planet either massive sediments containing enormous amounts of the various nitrogenous organic compounds, acids, purines, pyrimidines, and the like; or in much metamorphosed sediments we should find vast amounts of nitrogenous cokes. In fact no such materials have been found anywhere on earth [emphasis added].” Return to text.
  4. Even formation of the DNA ‘letters’ has major problems—see Sarfati, J., Origin of life: instability of building blocks, J. Creation 13(2):124–127, 1999 P-I-P-E creation.com/blocks; Nucleic acid bases in Murchison meteorite? Have they proved that life came from outer space? J. Creation 22(3):5–7, 2008 P-I-P-E creation.com/murchison. Return to text.
  5. Shapiro, J.A., A Third Way, Boston Review, p. 2, February/March 1997. Return to text.
  6. Newly Discovered DNA Repair Mechanism, Science News, sciencedaily.com, 5 October 2010. Return to text.
  7. Cf. Sarfati, J., Self-replicating enzymes? A critique of some current evolutionary origin-of-life models, J. Creation 11(1):4–6, 1997; creation.com/replicating. Return to text.

Helpful Resources

By Design
By Design
by Dr Jonathan Sarfati
US $15.00
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Chemicals to Living Cell
Chemicals to Living Cell
US $10.00
DVD

Readers’ comments

robert s.
AU March 5th, 2012
Is it possible that before the fall, the double helix in DNA was in fact a far more robust triple helix? [And a threefold cord is not quickly broken. Ecc 4:12] The basic diagram of the double helix looks like a three stranded rope with one strand missing. The connections between the strands of the double helix form a spiral ladder. The connections between three would form a far stronger series of triangles. Before we became corupted, we were properly in God's image; Father, Son and Holy Spirit, which could relate to a three sided triangle. Three strands in the rope and three connections between them. I am no scientist, but i was just wondering, since we seem to fall apart pretty quickly i.e. 70 years seems a bit short.
Jonathan Sarfati
March 6th, 2012
Dear Mr S.

Thank you for your comments.

I must say, I doubt it. DNA's function is not to be chemically robust, but to store and pass on information (see DNA: marvellous messages or mostly mess?. That would seem to require a double helix, where the strands can be separated and either be transcribed to RNA (sometimes but by no means always to be translated to a protein), or copied to more DNA for reproduction. Certainly, triple helical forms of DNA do exist, but their purpose is not really understood, although they might be involved in gene regulation by hindering transcription.

I doubt the Fall changed things like that, as opposed to God’s withdrawing some of His sustaining power. A change from triple to double would be a major redesign, yet the ordinary double helix is amazing enough.

I also caution against analogies to the Trinity in Nature, since they are inevitably cherry-picked. E.g. Binitarians could certainly point to the double helix, positive and negative charge, matter and energy, wave/particle duality, etc. And if I wanted to, I am sure I could find things for Quadrunitarians, such as the four dimensions of space-time, the Four Gospels, etc.

Actually, even 70 years is a long time, considering the number of DNA damages in each cell, and the number of cell divisions in a lifetime.

Regards

Jonathan Sarfati
John C.
January 15th, 2011
Without a doubt, this was one of the most fantastic articles I have seen produced on this web-site—and that’s saying something! The clips are not just interesting, they’re perfect! I hope to be able to direct some of my non-creationist friends to this site. May God bless you immeasurably for the great work you do.

Editor: We appreciate the encouragement that justifies the step of faith taken in committing thousands of dollars to having these animations specially made. Thank you also for publicizing our site. :)
Ian S.
January 15th, 2011
“But chemically, DNA is actually a very reactive molecule (and RNA is even more so), so it’s highly implausible that it could have arisen in a hypothetical primordial soup.”
False; the molecule itself is fairly inert, the atoms are highly reactive though which is why they form bonds in the way they do.

Editor: this is representative of a few queries—both friendly and hostile—on this matter. But the original researchers point out that this is a common misconception, as reported in Ref. 6:
“There is a general belief that DNA is ‘rock solid’—extremely stable,” says Brandt Eichman, associate professor of biological sciences at Vanderbilt, who directed the project. “Actually DNA is highly reactive.”
On a good day about one million bases in the DNA in a human cell are damaged. These lesions are caused by a combination of normal chemical activity within the cell and exposure to radiation and toxins coming from environmental sources including cigarette smoke, grilled foods and industrial wastes.
Alex Williams
AU January 15th, 2011
Recent imaging of the cell’s molecular machinery at single-atom resolution reveals even more cause for amazement. The atoms and molecules are vibrating (because of their heat energy)so rapidly that at 37°C (core temperature of the human body) only a blur can be seen. It is like watching a football match without being able to see any of the players, just a blur of colour. The vibration would destroy the machine if it were not built to work properly in this otherwise ‘impossible’ environment. ‘Correlated noise’ has also been observed to improve the function of nerve cells, which indicates that at least some biomachines are ‘tuned’ to resonate at the frequencies of their heat energy and thereby harness this ‘natural power’ source to achieve the incredibly high efficiencies of their energy transformations (almost 100% for ATP). Car engines operate with only about 20% efficiency, with 80% lost as heat.

Editor: thanks for this fascinating information.

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