DNA: the best information storage system
4 June 2015; updated 9 October 2015
Living creatures not only contain enormously complex machines, they also contain the ‘instruction manual’ to build these machines—which can be seen as a sort of ‘recipe book’ programmed on DNA, the famous ‘double helix’ molecule (deoxyribonucleic acid). In many articles and books, we have pointed out two of its remarkable features:
- Huge information storage capacity dwarfing that of the most advanced computer hardware.
- Surprising chemical instability.
Now some recent high-tech experiments on information storage have further vindicated our articles.
Encyclopedic information store
The information in DNA is spelled out using four different chemical ‘letters’: A, T, C, and G.1 These letters have a vital property which allows information to be transmitted: A pairs only with T, and C only with G. Due to the chemical structure of the bases, each pair is like a rung or step on a spiral staircase, the famous ‘double helix’ shape. Each DNA molecule has two strands, effectively the sides of the spiral staircase. The letter pairs form the steps, with A always opposite T and C always opposite G. The two strands can be separated and copied independently to form TWO spiral staircases, such that the new strands are exact copies of the original information.
The copying is far more precise than laboratory chemistry could manage, because there is editing (proof-reading and error-checking) machinery, again encoded in the DNA. This machinery keeps the error rate down to less than one error per 100 million letters.2 But, since the editing machinery itself requires proper proofreading and editing during its manufacturing, how would the information for the machinery be transmitted accurately before the machinery was in place and working properly? Lest it be argued that the accuracy could be achieved stepwise through selection, note that a high degree of accuracy is needed to prevent ‘error catastrophe’ in the first place—from the accumulation of ‘noise’ in the form of junk proteins specified by the damaged DNA.
Nowadays we would say that each of our cells—and there are about a hundred trillion in the human body—contains about three gigabytes of information.3 This is an incredibly high information density, about 1,000 terabytes per cubic millimetre (Tb/mm³).4 Even the simplest living creature, the tiny germ Mycoplasma, has about 600 kilobytes.5 And even its genome seems incredibly highly compressed. Some bioengineers, led by Stanford University’s Markus Covert, succeeded in modelling this ‘simple’ germ with computers.6 One report on trying to model the processes involved in one cell division for this cell stated:
“What’s fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell’s lifecycle processes.”7
In theory, without the constraints of cell function, DNA could store information at a density a thousand times more than in a cell, at a million Tb/mm³. If we could make a 1-gigabyte memory component using DNA, it would have a diameter thinner than a human hair.8
DNA is unstable
DNA is a very complicated molecule, and actually a very unstable one. DNA researchers often need to store it in liquid nitrogen, at –196°C (77 K; −320°F), and even that frigid temperature doesn’t entirely stop breakdown.
“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.”9
Fortunately, in our cells, we have many elaborate repair machines to undo this chemical damage.10 But most skeptics believe that life evolved in a primordial soup,11 which would have lacked such machines (not to mention the lack of any evidence that it existed at all12). So even if DNA managed to form spontaneously somehow, it would not have survived long.13
DNA in dino bones
For the past two decades,14 Dr Mary Schweitzer, although a committed (theistic) evolutionist herself, has been rocking the evolutionary/uniformitarian world with discoveries of soft tissue in dinosaur bones.15,16 These discoveries have included ligaments, blood and bone cells; flexible blood vessels;17 proteins like collagen,18,19 osteocalcin,20,21 actin, and histones, and most importantly, DNA.22,23 Her team detected DNA in three independent ways, including DAPI,24 which lodges in the minor groove of a DNA double helix. This shows that the DNA was quite intact, since short strands of DNA less than about 10 ‘letters’ don’t form stable duplexes.
However, a recent paper on DNA stability estimates that, even when preserved in bone, it would be completely disintegrated down to single ‘letters’ in 22,000 years at 25°C (77°F), 131,000 years at 15°C (59°F), 882,000 years at 5°C (41°F); and 6.83 million years at –5°C (23°F).25 Thus the researchers state:
“However, even under the best preservation conditions at –5°C, our model predicts that no intact bonds (average length = 1 bp [base pair]) will remain in the DNA ‘strand’ after 6.8 Myr. This displays the extreme improbability of being able to amplify a 174 bp DNA fragment from an 80–85 Myr old Cretaceous bone.”26
Note also, dinosaurs mostly lived in a warm climate, where DNA would break even more quickly, according to the above data.
DNA as computer information store
Computer manufacturers are always trying to increase the memory storage density of their hardware. Not surprisingly, some are looking to DNA because of its superlative qualities.
Another problem to be solved is data storage for the long term. Ordinary hard disk drives could not last more than a few decades, and are vulnerable to magnetic fields, high temperatures, and simply moisture and mechanical failure. Even the newer solid state drives must be connected to a power source or else their data will be lost in a few months.
It turns out that DNA might be the solution to this problem as well. Sure, it wouldn’t be able to stand the imagined evolutionary time scales, but it could well last longer than the above alternatives. Robert Grass and his team at prestigious university ETH27 Zürich (Switzerland) developed a promising technology.28
They first encoded 83 kilobytes of written information into 4,991 DNA segments each 158 ‘letters’ long. Such short segments are necessary because of the limits of current technology. By contrast, DNA molecules in our cells have from 50 million to 250 million ‘letters’.
Then they protected the delicate DNA by encapsulating it into 150-nanometer29 silica glass spheres—about the size of viruses. To recover the DNA, the spheres would be dissolved in a fluoride solution that doesn’t harm the DNA.
The real test was how long DNA would last. Obviously, tests lasting thousands of years are impractical, but it’s well known that reaction rate is strongly dependent on temperature.30 So time can be exchanged for temperature. The research term heated DNA at 60–70°C (140–160°F) for up to a month, which is equivalent to 10,000 years in a refrigerator at 4°C [40°F]. They found that 8% of the information was lost and most of the sequences had at least one mistake. But they also employed error checking codes, so the data could be recovered. If the DNA had been frozen to –18°C (0°F), it could have lasted over 2 million years.
This cutting-edge research underscores the awe-inspiring technology that our Creator has programmed into all living creatures. Since the best human computer technologists can’t beat it, they join it—they use the most compact information storage system known. The research also shows that even with highly artificial protection in nanoscopic silica balls, and by reducing the temperature to values much less than the areas in the world that generally contain dinosaur bones, DNA could not last as long as the evolutionary age of dinosaur fossils.
UpdateTo show the importance of these issues even in the secular scientific world, the 2015 Nobel Prize for Chemistry was awarded to three researchers for the discovery of the instability of DNA, which led scientists to realize that living things must have repair machinery.
Chemistry Nobel: Lindahl, Modrich and Sancar win for DNA repair
By Paul Rincon
Science editor, BBC News website, 7 October 2015
In the 1970s, scientists had thought that DNA was a stable molecule, but Prof Lindahl demonstrated that it decays at a surprisingly fast rate.
This led him to discover a mechanism called base excision repair, which perpetually counteracts the degradation of DNA.
Sir Martyn Poliakoff, vice president of the UK‘s Royal Society, said:Understanding the ways in which DNA repairs itself is fundamental to our understanding of inherited genetic disorders and of diseases like cancer. The important work that Royal Society Fellow Tomas Lindahl has done has helped us gain greater insight into these essential processes.
Turkish-born biochemist Aziz Sancar, professor at the University of North Carolina, Chapel Hill, US, uncovered a different DNA mending process called nucleotide excision repair. This is the mechanism cells use to repair damage to DNA from UV light—but it can also undo genetic defects caused in other ways.
People born with defects in this repair system are extremely sensitive to sunlight, and at risk of developing skin cancer.
The American Paul Modrich, professor of biochemistry at Duke University in North Carolina, demonstrated how cells correct flaws that occur as DNA is copied when cells divide. This mechanism, called mismatch repair, results in a 1,000-fold reduction in the error frequency when DNA is replicated.
References and notes
- Adenine, cytosine, guanine and thymine. They are part of building blocks called nucleotides, which are made up of three parts: the sugar deoxyribose, a phosphate, and a base (A, C, G, or T). In RNA, uracil (U) substitutes for thymine and ribose substitutes for deoxyribose. Return to text.
- Kunkel, T.A., DNA Replication Fidelity, J. Biological Chemistry 279:16895–16898, 23 April 2004. Return to text.
- For simplicity, I am treating each DNA ‘letter’ as a ‘byte’ of information, which is ‘in the right ball park’, and we have 3.17 billion base pairs (bp). In reality, since there are four possibilities at each locus, so it could store two bits of information per letter, and we have two copies of the genome in each cell, so 6.34 billion bp. Return to text.
- Borthine, D., DNA storage could preserve data for millions of years, gizmag.com, 18 February 2015. Return to text.
- Fraser, C.M., et al., The minimal gene complement of Mycoplasma genitalium, Science 270(5235):397–403, 1995; perspective by Goffeau, A., Life with 482 Genes, same issue, pp. 445–446. They reported 582,000 DNA bases or ‘letters’. Other reports have a different number, but all within the same ball park. Return to text.
- Karr, J.R. et al., A whole-cell computational model predicts phenotype from genotype, Cell 150(2):389–410, 20 July 2012. Return to text.
- Madrigal, A.C., To model the simplest microbe in the world, you need 128 computers, theatlantic.com, 23 July 2012. Return to text.
- ‘Ryan’, The amazing history of information storage: how small has become beautiful, numbersleuth.org, 30 August 2012. Return to text.
- Salisbury, D.F., Newly discovered DNA repair mechanism, Science News, sciencedaily.com, 5 October 2010. Return to text.
- Sarfati, J., New DNA repair enzyme discovered, creation.com/DNA-repair-enzyme, 13 January 2010. Return to text.
- For problems with materialistic ideas that life evolved from non-living chemicals, see creation.com/origin and Sarfati, J., By Design, ch. 11, 2008. Return to text.
- Brooks, J., and Shaw, G. point out, “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.” Origins and Development of Living Systems, p. 359, 1973. Return to text.
- Many skeptics believe that life started with a similar molecule called RNA (ribonucleic acid). But this is even less stable than DNA, and so are its building blocks such as the sugar ribose. John Horgan admits in ‘Scientists don’t have a clue how life began’ above, “But the ‘RNA-world’ hypothesis remains problematic. RNA and its components are difficult to synthesize under the best of circumstances, in a laboratory, let alone under plausible prebiotic conditions. … The RNA world is so dissatisfying that some frustrated scientists are resorting to much more far out—literally—speculation.” For those interested in chemistry, more chemical problems with ‘RNA World’ ideas can be found at creation.com/rna. Return to text.
- A good summary is Catchpoole, D., Double-decade dinosaur disquiet, Creation 36(1):12–14, 2014; creation.com/dino-disquiet. Return to text.
- Schweitzer, M.H. et al., Heme compounds in dinosaur trabecular bone, PNAS 94:6291–6296, June 1997. Return to text.
- Wieland, C., Sensational dinosaur blood report! Creation 19(4):42–43, 1997; creation.com/dino_blood. Return to text.
- Smith, C., Dinosaur soft tissue: In seeming desperation, evolutionists turn to iron to preserve the idea of millions of years, creation.com/dinosaur-soft-tissue, 28 January 2014. Return to text.
- Schweitzer, M.H. et al., Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis, Science 324(5927):626–631, 1 May 2009. Return to text.
- Wieland, C., Dinosaur soft tissue and protein—even more confirmation!, creation.com/schweit2, 6 May 2009. Return to text.
- Other researchers found osteocalcin ‘dated’ to 120 Ma: Embery G. and six others, Identification of proteinaceous material in the bone of the dinosaur Iguanodon, Connect Tissue Res. 44 Suppl 1:41–6, 2003. The abstract says: “an early eluting fraction was immunoreactive with an antibody against osteocalcin.” Return to text.
- Sarfati, J., Bone building: perfect protein, J. Creation 18(1):11–12, 2004; creation.com/bone. Return to text.
- Schweitzer, M.H. et al., Molecular analyses of dinosaur osteocytes support the presence of endogenous molecules, Bone 52(1):414–423 January 2013. Return to text.
- Sarfati, J., DNA and bone cells found in dinosaur bone, J. Creation 27(1):10–12, 2013; creation.com/dino-dna. Return to text.
- 4′,6-diamidino-2-phenylindole, a fluorescent stain. Return to text.
- Allentoft, M.E. et al., The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils, Proc. Royal Society B 279(1748):4724–4733,7 December 2012. Return to text.
- Allentoft et al., Ref. 25. Return to text.
- German: Eidgenössische Technische Hochschule = Federal Technical College. ETH Zürich is ranked 3rd best university in the world in engineering, science and technology. Return to text.
- Glass, R.N. et al., Robust chemical preservation of digital information on DNA in Silica with error-correcting codes, Angewandte Chemie [Applied Chemistry] 54(8): 2552–2555, 16 February 2015 | doi:10.1002/anie.201411378. Return to text.
- 1 nanometre (nm) = 10–9 m. A DNA strand is 2.5 nm in diameter. Return to text.
- Reaction rate depends exponentially on temperature, as per the famous rate equation formulated in 1889 by Swedish physical chemist and Nobel laureate Svante Arrhenius (1859–1927). This the rate constant (k) of a chemical reaction to absolute temperature (T) and activation energy Ea: k = A exp (–Ea/RT), where R is the universal gas constant and A is an experimentally determined constant. Return to text.