Rapid Bedrock Incision by Water Stream Outburst: The Case of the Oroville Dam (California, USA)

New observational data on the phenomenon of rapid bedrock erosion became recently available after the well documented events that affected the Oroville Dam in February 2017.

The Oroville Dam, located in northern California, USA, confines a large water reservoir (Lake Oroville) with a retention capacity of about 4 km3. The lake level is controlled through a main spillway, consisting of a concrete chute nearly 1 km long and about 50 m wide that slopes for over 200 vertical meters down to the Feather River (Fig. 1). An emergency spillway, designed to be active in cases of extremely high lake levels, is located to the side (NW) of the main spillway, and consists of a linear concrete weir separating the lake waters from the wide valley flank that leads down to the river bed (Fig. 1).

Fig 1: Map view sketch (A) and oblique aerial photo (B) of the Oroville Dam and its spillways. Left image by Shannon1, available at https://en.wikipedia.org/wiki/Oroville_Dam_crisis#/media/File:OROVILLE_DAM_1.svg (CC BY-SA 4.0). Right photo by K. M. Grow, California Department of Water Resources, taken on May 11, 2016, several months before the spillway incident. Note how the emergency spillway is faced by a vegetated slope with no artifacts or structures to confine flow or control erosion in case of spilling.

The Crisis in February 2017[i]

Exceptional rainfall in the Winter of 2017 caused significant inflow into the reservoir and required activation of the main spillway to control the lake level. On February 7, an irregular flow behavior was detected in the middle part of the main spillway chute. Water discharge was interrupted to investigate the cause of the anomaly, revealing that the concrete chute was severely damaged over tens of meters. A large section of concrete had been washed away and water had already created an erosional path to the left (SE) of the chute (Fig. 2). However, because of increasing lake levels caused by exceptional rainfall, discharge on the damaged spillway was reactivated on February 9, with outflow rates varying between of 1120 and 1820 m3/s. In spite of this renewed outflow, the lake level kept rising, reaching more than 901 feet on the night between February 11 and 12, and causing overflow at the weir of the emergency spillway for the first time in the history of the dam (Fig. 3).

Fig 2: Map view sketch (A) and oblique aerial photo (B) of the damage and erosion observed on the main spillway of the Oroville Dam, on February 7, 2017. Left image by Shannon1, available at https://en.wikipedia.org/wiki/Oroville_Dam_crisis#/media/File:OROVILLE_DAM_3.svg (CC BY-SA 4.0). Right photo by K. M. Grow, California Department of Water Resources. Dashed line indicates damaged area. White arrow points to car, for scale.

 

 

Fig 3: (A) Map view sketch of water flows at the Oroville Dam on February 12, 2017. An exceptionally high lake level triggered overflow at the emergency spillway. Image by Shannon1, available at https://en.wikipedia.org/wiki/Oroville_Dam_crisis#/media/File:OROVILLE_DAM_4.svg (CC BY-SA 4.0); (B) View of overflow at the emergency spillway and incipient erosion of soil cover and bedrock downstream of the weir. Photo by K. M. Grow, California Department of Water Resources, taken on February 12, 2017.

Erosion downhill of the emergency spillway occurred faster and more effectively than expected, with the threat of possible collapse of the weir and consequent catastrophic release of large volumes of water. This risk prompted a mandatory evacuation of the Oroville area (about 200,000 inhabitants), on February 12. Decision makers managing the crisis had to significantly increase the outflow rate at the main spillway (to 2800 m3/s) to bring the lake level below the threshold of the emergency spillway. This would imply further erosion and damage at the main spillway, but it was estimated that the new incision next to the spillway would deepen in a “controlled” manner, preventing sheet erosion or another lateral breakout towards the dam. The strategy worked, and on the night between February 12 and 13 the overflow at the weir of the emergency spillway stopped (Fig. 4). As the lake level kept decreasing, discharge at the main spillway was also gradually reduced until, on February 27, the outflow was finally halted to begin the subsequent phases of surveying, cleanup, and repair.[ii]

Fig 4: (A) Map view sketch of main erosional and water flow features at the Oroville Dam after overflow at the emergency spillway was stopped. 1 = area where crews started to work from February 13 to reinforce the partially damaged weir; 2 = erosion and bedrock incision downhill of the emergency spillway; 3 = zone of accumulation of debris from erosion and bedrock incision along main spillway, causing upstream blockage of the Feather River and interruption of functionality of the power station. Image by Shannon1, available at https://en.wikipedia.org/wiki/Oroville_Dam_crisis#/media/File:OROVILLE_DAM_5.svg (CC BY-SA 4.0); (B) View of channelized flow pattern diverting from damaged main spillway and confined to newly incised canyon. White arrow points to channelized incision created on February 12 by water outflow from the emergency spillway. Yellow arrow points to river bar consisting of debris accumulated from the erosion occurring at the main spillway. Photo by K. M. Grow, California Department of Water Resources, taken on February 26, 2017.

Remarks and Implications

The extent of erosion attained in just a few days at the main spillway is remarkable. The concrete spillway chute was destroyed and torn away in its middle to lower section. Next to the chute, a canyon was incised, several tens of meters deep and several hundred meters long (Figs. 4B, 5A). Overflow from the emergency spillway removed soil cover and caused significant bedrock incision in just one day (Figs. 4B,5B).

Fig 5: (A) View of the effects of erosion at the main spillway. Middle to lower section of the concrete chute is missing or damaged and a deep canyon has been incised to the SE of the chute. Photo by D. Kolke, California Department of Water Resources, taken on February 27, 2017; (B) Channelized incision downstream of the emergency spillway, generated in approximately 1 day of outflow. Arrow points to person for scale. Photo by F. Low, California Department of Water Resources, taken on February 18, 2017.

 

The bedrock in the area affected by erosion is part of the Jurassic Smartville Complex, and consists of low grade metavolcanics of mafic composition, with sheeted diabase intrusions.[iii] The tabular nature of the volcanics and of the subsequent sheeted intrusions confers a distinctively layered aspect to the unit. Layers dip at a relatively high angle to the east, against the slope of the valley (Fig. 6). The planar discontinuities of the layering and some fractures favored plucking of blocks as the main mechanism of erosion under solicitation by hydraulic flow, as demonstrated by the abundance of planar faces on the angular blocks in the debris pile and on the jugged surface of the eroded bedrock (Fig. 7).

Fig 6: Bedrock exposed after erosion at the main spillway. High angle layering highlighted by black dashed line. Arrow points to group of people on concrete chute for scale. Photo by F. Low, California Department of Water Resources, taken on March 3, 2017.

 

Fig 7: (A) Angular blocks of bedrock accumulated on the bed of the Feather River, downstream of the main spillway. Photo by B. Baer, California Department of Water Resources, taken on March 1, 2017. (B) Outcrop showing flat faces and sharp edges suggestive of bedrock plucking, next to damaged concrete of the main spillway. Photo by F. Low, California Department of Water Resources, taken on March 4, 2017.

Weathered bedrock (yellowish brown color) is certainly less competent than the fresh lithology (bluish-green color), and spatial variations in thickness of this top level might have played a role in determining the points where extensive erosion was initially concentrated. However, significant fresh bedrock erosion took place both at the main spillway and downhill of the emergency spillway (Figs. 5-8).

Fig 8: (A) Both fresh and altered bedrock is exposed along the incision path downstream of the emergency spillway. Photo by D. Kolke, California Department of Water Resources, taken on February 15, 2017. (B) Both fresh and altered bedrock has been eroded under the main spillway. Photo by F. Low, California Department of Water Resources, taken on March 3, 2017.

 

The debris generated by erosion at the main spillway (an estimated 1 million tons of material) accumulated at the foot of the new canyon, rapidly creating a system of coarse-grained, boulder-rich bars at the confluence with the Feather River (Fig. 9).[iv]

Fig 9: Coarse-grained fluvial bar generated at the confluence between the new incised canyon by the main spillway and the Feathered River, before (A) and after (B) halting water discharge through the spillway. Photos by D. Kolke, California Department of Water Resources, taken on February 27, 2017.

At the beginning of the crisis, there had been fears that the service spillway, initially damaged in its middle section (Figs. 2B,10A), would be affected by back-stepping erosion and collapse, thus attacking the dam itself. In fact, this happened at first (Fig. 10B), but most incision seems to have concentrated in the narrowed flow cross-section of the newly cut canyon next to the chute, with relatively minor headward propagation of erosion (Fig. 10C).

Fig 10: Damage on the chute of the main spillway at three different times during the crisis. Horizontal yellow line is given as a reference point across the three images. Black arrow in (C) points to person for scale. Original photos by K. Grow (A,B) and F. Low (C), California Department of Water Resources, taken on February 7, February 9, and March 3, 2017, respectively.

 

The initial cause of the damage at the main spillway, as well as the extent and mechanisms of subsequent erosion will be thoroughly investigated by engineers and geologists. Here appropriate technical and professional publications are to be expected.

The maximum flow or discharge rate attained in the bedrock incision at the main spillway – 2800 m3/s, reduced by the proportion of water that kept flowing over the chute – is comparable to smaller Icelandic glacial outburst floods (jökulhlaups), which have rates of 103 to 104 m3/s, and some orders of magnitude lower than a megaflood with rates of ≥ 106 m3/s.[v]

This event of observed erosion provides the rare opportunity to analyze the formation of a canyon and test models used to account for large-scale erosional features of the landscape. After all, the idea is still widespread that deep river canyons (e.g., Grand Canyon of Colorado) formed over prolonged geologic time by slow and gradual fluvial incision; in contrast, there are observational data that suggest the possibility of canyon formation during high-energy and rapid erosive events.[vi] Most importantly, the observation of bedrock erosion and formation of depositional bars over short time scales in a relatively localized area is a powerful miniature representation of what could be expected in the context of non-uniformitarian, large-scale water flows.


Endnotes

[i] An informative graphical and descriptive timeline of the events can be found in this report from the California Department of Water Resources: “Lake Oroville Spillway Incident: Timeline of Major Events February 4-25“; accessed on 09/20/2018.

[ii] Video clips showing the different phases of the crisis and the subsequent reconstruction efforts can be watched on the Oroville Spillway Incident YouTube page of the California Department of Water Resources.

[iii] Saucedo, G.J., Wagner, D.L., (1992). Geologic map of the Chico quadrangle, Regional Geologic Map 7A, California Division of Mines and Geology. Day, H.W., Bickford, M.E. (2004). Tectonic setting of the Jurassic Smartville and Slate Creek complexes, northern Sierra Nevada, California. GSA Bulletin, 116, 1515–1528.

[iv] For another example of rapid formation of coarse fluvial bars during flooding conditions, see Mosher, S.‐J., Martini, I. P. (2002). Coarse‐grained flood bars formed at the confluence of two subarctic rivers affected by hydroelectric dams, Ontario, Canada. In: Martini, I.P., Baker, V.R., Garzón, G. (eds.), Flood and Megaflood Processes and Deposits: Recent and Ancient Examples. International Association of Sedimentologists Special Publication 32, Wiley-Blackwell, Oxford, UK, pp. 213-231.

[v] See Baker, V.R. (2013). Global late Quaternary fluvial paleohydrology: With special emphasis on paleofloods and megafloods. In: Shroder, J., Wohl, E.E., (eds.), Treatise on Geomorphology, Fluvial Geomorphology, vol. 9, Academic Press, San Diego, pp. 511-527; Kotulla, M., (2014). Megafluten. Studium Integrale Journal 21, 4-11.

[vi] For a detailed discussion, see Ernst, M. (2010). Bildung eines Canyons in nur 3 Tagen. Studium Integrale Journal 17, 88-92.


Michael Kotulla, Dipl.-Geol.,
Studiengemeinschaft Wort und Wissen e. V., Baiersbronn, Germany

Ronny Nalin, PhD,
Geoscience Research Institute, Loma Linda, USA

Posted in Catastrophism, Geology | Tagged , , , , , , , | Leave a comment

Pterosaurs of the Triassic: An Update

This post complements an article that was originally written in 2014, and can be found here. Since then, there have been some interesting developments in the area of Triassic pterosaurs that are worth mentioning, the most important being the recent description by Britt et al. (2018) [1] of a Triassic pterosaur from the Nugget Sandstone of Utah.

This species, dubbed Caelestiventus hanseni, is very similar to the Jurassic genus Dimorphodon (Fig. 1), making it the first definitive Triassic member of the family Dimorphodontidae (Peteinosaurus may or may not be a dimorphodontid). Despite the similarities to Dimorphodon, Caelestiventus is bizarre in its large, leaf-shaped, laterally-compressed teeth on the upper jaw. Laterally-compressed teeth are rare for pterosaurs, although they have been documented in other Jurassic and Cretaceous groups (McLain and Bakker, 2017) [2].

Fig. 1: A cast of the skeleton of Dimorphodon, a Jurassic pterosaur in the same family as the newly discovered Triassic form Caelestiventus. Image from Wikipedia, courtesy of MCDinosaurhunter (CC BY-SA 3.0).

The most remarkable thing about Caelestiventus is that it was found in a deposit that has been interpreted to have been an ancient desert. The large crossbeds within the Nugget Sandstone are assumed to have been laid down by wind-blown dunes. However, this assumption may be misplaced, as another famous “desert” sandstone – the Permian Coconino Sandstone – has been argued from multiple strong lines of evidence to have actually formed underwater (Whitmore and Garner, 2018) [3].

Another relevant change in the taxonomy of Triassic pterosaurs is that “Eudimorphodon cromptonellus has now been placed into its own genus: Arcticodactylus (Kellner 2015) [4]. In the same paper, Kellner also named BSP 1994 I 51 as Austriadraco dallavecchiai and named a “Eudimorphodon” specimen (MPUM 6009) Bergamodactylus wildi. However, Dalla Vecchia (2018) [5] concluded that Bergamodactylus is actually just a skeletally immature Carniadactylus. Surprisingly, Kellner noted a very unique feature in Austriadraco, which is previously unknown in any other pterosaur: a hole in the lower jaw called an external mandibular fenestra.

The published phylogenetic tree in Britt et al. (2018) [1] shows with even greater clarity the claims that were made in the  2014 blog post: Triassic pterosaurs show up in the fossil record already diverse, with at least four separate clades [Dimorphodontidae, Eudimorphodontidae, Austriadraconidae (unnamed in the paper), and Preondactylus + Austriadactylus] and Peteinosaurus represented. Rather than finding a trunk to the pterosaur evolutionary tree, fossil discoveries continue to show pterosaurs of the Triassic to be fully-formed and remarkably diverse.

References

[1] Britt, B.B., Dalla Vecchia, F.M., Chure, D.J., Engelmann, G.F., Whiting, M.F., and Scheetz, R.D. 2018. Caelestiventus hanseni gen. et sp. nov. extends the desert-dwelling pterosaur record back 65 million years. Nature Ecology & Evolution 2:1386-1392.

[2] McLain, M.A. and Bakker, R.T. 2017. Pterosaur material from the uppermost Jurassic of the uppermost Morrison Formation, Breakfast Bench Facies, Como Bluff, Wyoming including a pterosaur with pneumatized femora. New Perspectives on Pterosaur Palaeobiology. Geological Society, London. Special Publications 455.

[3] Whitmore, J.H. and Garner, P.A. 2018. The Coconino Sandstone (Permian, Arizona, USA): Implications for the origin of ancient cross-bedded sandstones. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 581-627. Pittsburgh, Pennsylvania: Creation Science Fellowship.

[4] Kellner, A.W.A. 2015. Comments on Triassic pterosaurs with discussion about ontogeny and description of new taxa. Anais da Academia Brasileira de Ciências 87(2):669-689.

[5] Dalla Vecchia, F.M. 2018. Comments on Triassic pterosaurs with a commentary on the “ontogenetic stages” of Kellner (2015) and the validity of Bergamodactylus wildi. Rivista Italiana di Paleontologia e Stratigrafia 124(2):317-341.


Matthew McLain, PhD
Assistant Professor of Biology and Geology
The Master’s University

Posted in Evolutionary Theory, Fossils, Pterosaurs | Tagged , , , , , | 1 Comment

Is there biological evidence of life’s recent creation?

During one of my frequent visits to the office of my high school headmaster, his individual tutelage yielded a life lesson that I’ve never forgotten. His exact words were, “You think you’re right!” Of course I thought I was right, wouldn’t anyone who thought they were wrong change their mind and then immediately think they are right?

Now that I’m an adult biologist, I still think that I’m right. Inevitably that means I disagree with some other people’s opinions; it is the price I and they pay for being thinking human beings. I think I’m right when I believe that that astrologers can’t tell the future, that priests can’t create the actual body and blood of Christ during the Mass and that geologists can’t really know with certainty that life has existed on Earth for billions of years.

When it comes to the age of life, no human was there to actually see it created, so we have to rely on our interpretation of the evidence. Interestingly, there is one eyewitness account, written in stone by the witness Himself. The 4th Commandment in Exodus 20 and 31 records what God wrote with his own finger: “ for in six days the Lord made the heavens and the earth, and on the seventh day He rested and was refreshed” (Exodus 31:17 NKJV). That may not tell us the exact date of the creation, but it does clear up any reasonable question about how long it took, at least according to God.

There is evidence in the Bible of when the creation occurred. It involves adding up the age at which fathers had children and figuring out a reasonable starting point to count back from. In addition, there are things like the genealogy of Jesus stretching all the way back to Adam (Luke 3:23-38) which tie into the more ancient genealogies. Scholars have figured out lots of different ways of adding the numbers, but those who stick with things like logic and data find it difficult to get a biblical creation date more than a few thousand years ago.

Do I as a biologist think that the scientific data point in the same direction? The simple answer is yes. I know, this is tantamount to heresy among those who believe they have it right that life is billions of years old; but when I look at the most informative data most carefully, I see that the scientific evidence, at least in my field, is quite consistent with the biblical record. If you want to know how old something is, first of all you should look at it. The right place to start when investigating when life came into existence, is by looking at living things.

So, let’s look at 5 lines of evidence from living (and dead) things to see what they suggest about how old life is. Let’s start with dinosaurs, because everyone knows they are cool and that they lived tens of millions of years ago… except for me and some others who are looking at the evidence they have left behind.

Evidence 1-Ancient biomolecules[1]

Dinosaur bones embedded in sediment; scale is 40 cm long. Dinosaur Ridge, CO, USA.

Dr. Mary Schweitzer did something that anyone who knew about fossil dinosaurs wouldn’t have done. She took a fragment of dinosaur bone and put it into a solution that dissolved away the minerals. This is similar in principle to the classic experiment of putting a chicken bone in vinegar. When the mineral component of the bone is dissolved in the vinegar, the protein component is left behind and you can tie the bone in a knot without breaking it. The problem with what Dr. Schweitzer did is that everyone knows that there could be no protein component left in dinosaur bones because proteins don’t last for tens of millions of years.

Proteins, DNA and other big biological molecules are broken by water, oxygen and other chemicals. In addition, they are broken by radiation and, while there isn’t much radiation over the course of a day, over the course of millions of years it really adds up. At least in theory, there should be no protein in dinosaur bones if they are tens of millions of years old. Of course, theory isn’t the same as observation, but when we study modern bones, their proteins break down. Presumably proteins in bones broke down in the past as well.

Knowing that there should not be proteins in dinosaur bones, you can hardly imagine the shock when Dr. Schweitzer reported that there was abundant protein in her dinosaur bone samples. The most reasonable explanation would seem to be that the bones are not millions of years old. However, some scientists, including Dr. Schweitzer, have suggested that maybe proteins are preserved in the presence of iron, or when they are associated with the mineral part of bone material. These explanations seem quite optimistic. In addition, it isn’t just protein that has been found associated with fossils, other biological molecules have also been found and I, along with some colleagues, have accumulated hundreds of papers about this from the peer reviewed scientific literature. At least from my perspective as a biologist, suggesting that proteins and other biological molecules have lasted for tens of millions of years is equivalent to claiming a miracle. It is surprising enough that they could have lasted thousands of years buried in the ground.

Evidence 2-Mutations[2]

Every now and then, the chemical letters in DNA molecules are changed. These changes are called mutations and they may be caused by chemical damage to DNA, viral infections, radiation or errors in copying DNA. Mutations are a problem, because DNA contains the recipes for how, when and where to make the proteins in our bodies. Randomly change the recipes and things can go very wrong.

The good thing is that the information encoded in our DNA is remarkably robust, so most of the time, mutations don’t kill us, at least immediately. When a mutation is really bad, generally the person with it dies, so it isn’t passed on to their children. But what about those mutations that are just a little bit negative, but don’t kill you? These are called “near neutral” mutations and, while they don’t immediately kill people, they are not weeded out by natural selection and so they accumulate in human’s DNA.

There are different estimates of how fast mutations are accumulating, but commonly they run above 100 mutations per person per generation. It is good thing that most mutations are near neutral, but they are still thought to have a small cumulative negative effect. At our current mutation rate, eventually, the recipes for the vital proteins in our bodies will inevitably be corrupted to the point that we can’t survive.

Humans are thought to be in something called “error catastrophe,” which means that we are mutating so fast that the human race can’t last forever. The same is probably true for other organisms. So, if we can’t last forever, how long can we last? Time will tell, but millions of years seems way too optimistic. It thus seems depressingly obvious that humans and other organisms probably haven’t been around for millions of years and are unlikely to last too many thousands of years longer. Even unbelievers should be hoping that Jesus comes soon and does a new creation; otherwise, we have little hope for the future.

Evidence 3-Improbable hybridizations[3]

A London plane tree, thought to have originated from hybridization between Platanus occidentalis and Platanus orientalis. Kew Gardens, England.

A gardener working in the Oxford Botanical Gardens around 1670 AD, noticed some tree saplings coming up that he had never seen before. It turned out that these new trees were the result of hybridization between American sycamore trees, Platanus occidentalis, and oriental plane trees, Platanus orientalis, whose native range extends from the Balkans to Iran.

This may not seem impressive. After all, these are trees in the same genus and they don’t appear to be very different, but these species normally grow more than 5,000 km apart. The continents they are native to are supposed to have separated something more than 50 million years ago. So, these are species that should have been on their own different paths of evolution for tens of million years. That is the kind of timespan that Darwinists typically invoke to explain the evolution of humans, chimpanzees, old world and new world monkeys from some kind of primitive monkey.

The idea that two organisms could be separated by thousands of kilometers and tens of millions of years, yet still be capable of interbreeding, seems incredible, and it seems even more incredible from a Darwinian perspective than from a Biblical perspective. There are alternative and more reasonable explanations. The most obvious is that these two species are not separated by tens of millions of years. This may be because life isn’t millions of years old, or it may be that what became the American sycamore was transported in the relatively recent past from the Middle East to what is now the United States. Or maybe the American Sycamore was transported to the Middle East. In either case, there is no 50 million years.

Explanations to maintain the idea of millions of years get progressively more heroic as more and more unexpected hybridizations are discovered, and these are not difficult to find. For example, male jaguars from the New World will mate with female lions from the Old World to produce heathy jaglions.

Evidence 4-Interchangeable parts[4]

The cells of all organisms are teeming with a wide variety of nanomachines performing all the functions necessary to keep cells alive. Do these molecular machines, which operate with incredible speed and efficiency, look as if they evolved in different kind of organisms over hundreds of millions or billions of years?

Imagine driving a Ford Focus with a damaged headlamp assembly. It would be surprising to find out that the headlamp could be replaced with one from the previous Focus model and preposterous to believe it could be replaced with the headlamp from a Model-T Ford. Yet, interchangeably like this is exactly what we see in cells.

A good example is a molecular machine called Signal Recognition Particle (SRP), which plays a vital role in production of the proteins found in membranes. SRP is made up of a stretch of RNA—a molecule similar to DNA—and several proteins. It turns out that the protein and RNA components of SRP are interchangeable between an extraordinary range of organisms. Human SRP proteins form functional SRPs when combined with the RNA component of Xenopus laevis (frogs) or Drosophila (flies). Replacing one major component of Canis familiaris (dog) SRPs with the single large SRP protein from a bacterium called Escherichia coli, makes a SRP functional in all respects except for binding to the endoplasmic reticulum receptor. The corresponding dog SRP protein can bind to the RNA portion of E. coli SRP.

Data like these are well explained by a model in which a designer uses standard parts to make different machines and these machines have not drifted apart over time. The idea that modern dogs and bacteria separated from a common ancestor a billion or more years ago and went through the extraordinary changes necessary to produce the organisms we observe today, yet retain interchangeable molecular parts seems incredible. By comparison, recent creation of life seems quite reasonable. Both require miracles, but maintaining interchangeable parts over a billion years seems a very long and complex miracle compared to a recent creation.

Evidence 5-Carbon-14[5]

Radiometric dating is commonly seen as one of the strongest argument that life is millions or billions of years old. In this technique, the concentrations of unstable atomic isotopes and their daughter products produced upon breaking down should indicate the age of a sample. Because these isotopes are thought to break down at a constant rate, a sample with very little of the unstable isotope and an abundance of the daughter products should be old.

When measuring the age of biological things, the most obvious isotope to use is Carbon-14. This is very similar to the regular carbon we find in diamonds, graphite and the chemicals that make up living things, the only difference being that it has two extra neutrons in its nucleus.

Carbon-14 breaks down fairly slowly so that half of the Carbon-14 in a sample will be gone after about 5,700 years. After another 5,700 years, half of the remaining Carbon-14 will be gone and so on for every passing 5,700 years. After about 20 5,700 year increments (114,000 years) only one millionth of the original Carbon-14 will be left in the sample. As there is very little Carbon-14 in the first place, by the time a sample is over 100,000 years old, there should—at least theoretically—be too little Carbon-14 to measure.

This is where things get interesting. It turns out that Carbon-14 has been measured in coal and other biological samples that are supposed to be tens to hundreds of millions of years old. Most reasonably, these data mean that the plants used to form the coal lived within the past 100,000 years.

Example of a coal bed, from the Bulli Coal Measures, New South Wales, Australia.

What does a Darwinist who believes life is millions or billions of years old to do with these data? Generally, the response is that the Carbon-14 detected is a consequence of contamination, or that it was somehow generated within the samples. There are responses that could be made to these responses, but they get progressively more technical. If nothing else, this situation illustrates that it is common for people to reject radiometric dates, like Carbon-14 dates, when they do not agree with their prior ideas about the way things must be.

Conclusions

This is not supposed to be an exhaustive list of all the possible scientific evidence consistent with life’s recent creation. No doubt, there are many other evidences which could be added, but I find these data to be informative.

When we evaluate scientific theories, it is essential to remember that empirical data are the final word. Time prevents empirical observation of life’s origin, which means we can only interpret the current data. It is important to keep in mind that the further interpretation is from data, the greater the number of necessary assumptions, the greater the number of logical steps, the less certain the conclusion.

In my experience, evidence interpreted within a biblical framework requires an equal number, or fewer, assumptions and logical steps than interpretations requiring long expanses of Darwinian time. Everyone who wishes to know what is true will have to figure this out to some degree for themselves. In doing this, independent thinking is invaluable. Of course you will think that you are right most of the time, but one should never be so sure of that that they are unwilling to consider the most informative data carefully and, perhaps, change their mind. I know that I have had to do that multiple times and I think I was right to do so. Living life as a Christian scientist doesn’t mean starting out with all the right answers, it means a humble quest for knowledge in a world that is beautiful, full of wonder, constantly surprising and brimming with mysteries. We may not have all the answers all the time, but it is reassuring to see how often reasonable interpretation of the data we observe is consistent with the record of history in God’s Word.

Endnotes

[1] Mary Schweitzer’s first paper on this topic was: Schweitzer MH, Wittmeyer JL, Horner JR, Toporski JK. 2005. Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rex. Science 307:1952-1955. Further examples along the same lines include: Schweitzer MH, Wittmeyer JL, John R. Horner JR. 2005. Gender-Specific Reproductive Tissue in Ratites and Tyrannosaurus rex. Science 308:1456-1459; Schweitzer MH, Zheng W, Cleland TP, and Bern M. 2012. Molecular analysis of dinosaur osteocytes support the presence of endogenous molecules. Bone, 2012; DOI. 10.1016/j.bone.2012.10.010; Analysis of dinosaur bone cells confirms ancient protein preservation, Science Daily, October 23, 2012; Hofreiter M, Collins M, and Stewart JR. Ancient biomolecules in Quaternary palaeoecology. Quaternary Science Reviews, 33, 6 February 2012, p. 1-13.

[2] An excellent discussion of this evidence can be found in: Sanford JC. 2014. Genetic Entropy 4th Ed. FMS Publications.

[3] While other theories of the origin of London plane trees exist, there is consensus that this tree represents a hybrid between the American sycamore and Oriental plane tree. The source most reasonably referenced on the Oxford origin is: Flood AH, Flood MG. 1919. The History of the London Plane, Platanus Acerifolia, with Notes on the Genus Platanus. Proceedings of the Royal Irish Academy. Section B: Biological, Geological, and Chemical Science 35:9-28. Estimations of the relationships between and times of separation can be found in: Feng Y, Oh S-H, Manos PS, Zomlefer WB. 2005. Phylogeny and Historical Biogeography of the Genus Platanus as Inferred From Nuclear and Chloroplast DNA. Systematic Botany 30(4):786-799.

[4] Many examples of this phenomenon could be referenced, but the specific Signal Recognition Particle examples can be found at: Walter P, Blobel G. 1983. Disassembly and reconstitution of signal recognition particle. Cell 34:525-533; Bernstein HD, Zopf D, Freymann DM, Walter P. 1993. Functional substitution of the signal recognition particle 54-kDa subunit by its Escherichia coli homolog. Proceedings of the National Academy of Sciences USA. 90:5229-5233; Romisch K, Webb J, Lingelbach K, Gausepohl H, Dobberstein B. The 54-kD protein of signal recognition particle contains a methionine-rich RNA binding domain. Journal of Cell Biology 111:1793-1802; Zopf D, Bernstein HD, Johnson AE, Walter P. 1990. The methionine-rich domain of the 54 kd protein subunit of the signal recognition particle contains an RNA binding site and can be crosslinked to a signal sequence. EMBO Journal 9(13):4511-4517.

[5] This is now a widely recognized phenomenon. A good reference is: Baumgardner JR. 2005. Carbon-14 Evidence for a Recent Global Flood and a Young Earth. Chapter 8 in: RATE II: Radioisotopes and the Age of The Earth: Results of a Young-Earth Creationist Research Initiative, Volume II, L. Vardiman et al., eds. Institute for Creation Research and the Creation Research Society: San Diego, CA.


Timothy G. Standish, PhD
Senior Scientist, Geoscience Research Institute

Posted in Biogeography, Biology, Dating and the Age of the Earth, Dinosaurs, Evolutionary Theory, Molecular | Tagged , , , , , , , , , , , , , , | Leave a comment

A Physicist’s Look at Nature and the Nature of God

God is transcendent, therefore He cannot be properly illustrated by anything that belongs to the creation. A simple example suffices to make this point. Since God in His nature is eternal and uncreated, there can be nothing in His created universe that qualifies to illustrate both these characteristics.

Yet, because the creation of God bears undeniable evidence of its Author, there are things in nature that may reflect – even though in a very pale way – some of the characteristics of the nature of God. What follows are two analogies from physics that can serve as illustrations for aspects of the Divinity, starting from the premise that what we can know of God is founded on what He Himself has revealed to us through the Holy Scriptures. Therefore, our endeavor to grasp a vision of God through His creation will be directed and restricted to what the Scriptures reveal about the nature of God, for what goes beyond that is pure speculation.

1) Love, the Trinity, and protons

The most prominent characteristic of God revealed to us in the Bible is that God is love (1 John 4:8, 16). Love is the very essence of the nature of our Creator. The moment we mention love, we immediately make an association with intimate, meaningful relationships. These, by their very nature, presuppose the existence of at least two persons involved, for love cannot manifest itself if there is only one person and acquires meaning only when expressed toward someone else. Therefore, if God is love, the only One God and LORD has to consist, at the same time, of distinct persons – Father, Son and Holy Spirit – as the Scriptures reveal.

The unity of the triune God – One, but at the same time Three – is very difficult to grasp for our finite minds. I have read of someone with a mathematician’s mind reason that God’s triune nature is not to be understood as a sum of three persons, “1+1+1=3,” but rather as a multiplication of them, “1x1x1=1.”

I find an appropriate illustration for the triune nature of God deep inside the atom, in its core nucleus. Physicists trying to understand the basic constituents of the physical world came to recognize that baryons – particles like protons and neutrons that compose the nucleus of all atoms – are made up of quarks. Quarks are elementary particles that are perpetually “confined” inside baryons. There are three unique constituent quarks in baryons, inseparably bound together by so called gluons in such a way that the more energy is used in trying to separate them, the more tightly they become bound (Fig. 1).

Fig. 1: Idealized representation of a proton, composed of two up quarks, one down quark, and the gluons (symbolized by springs) that mediate the forces “binding” them together. Image by Jacek Rybak (CC BY-SA 4.0).

Of course, we can hit a proton with another proton having an amount of energy so great that the bullet proton and the target proton both break down (disappear) – but surprisingly, the six composing quarks (three from each proton) cannot be “seen,” that is, cannot be detected as such: they become tightly reunited to each other again to become part of confined quarks of other particles that are produced! Moreover, protons are stable particles, that is, left by themselves they can remain forever! So, in my modest attempt at illustrating the triune nature of God, I like to use the analogy of the sub atomic, nuclear particle proton, which is part of the core of the visible matter in the universe: one but composed of three inseparable quarks. 

2) Jesus as Light of the world

It is not without reason that theologians have grappled with the ‘problem’ of the nature of Jesus since He was born into humankind, or as the Scriptures say, “He became flesh.” John 1:1 affirms categorically that Jesus is God. On the other hand, the apostle Paul says that the Mediator between God and humankind is “the man Christ Jesus” (1 Timothy 2:5). So, was Jesus God? Or was He Man? Or was He both God and Man? And if so, in what sense was He both God and Man?

In trying to understand the nature of Jesus it is important to focus on what Jesus said of Himself. In this way we may remain safely within the grounds of what has been revealed to us. In John 8:12 Jesus said: “I Am the light of the world”. We can delve deep into this imagery both spiritually and practically to extract some wonderful lessons.

First of all, consider how without light there can be no life. On planet Earth, we are all dependent upon the light that comes from the sun, which is the source of the energy that is transferred – amongst other things – into the food we eat and the fuels we use. Thus, in the same way, without Jesus there can be no life. Life is not only a gift from God, but its continuance is warranted only because God sustains it constantly by His power and will. He not only is the light of the world, but He is the Source of light – hence the appropriateness of the name Sun of Righteousness attributed to Jesus: “But to you who fear My name the Sun of Righteousness shall arise with healing in His wings; and you shall go out and grow fat like stall-fed calves” (Malachi 4:2).

Modern physics has to deal with two seemingly incompatible concepts of classical physics: the particle-like and wave-like character of light. Thus we talk about the “wave-particle duality” when referring to the nature of light. What does it mean to say that light has this dual nature? Well, as bewildering as it may be, light behaves like a wave (it is an electromagnetic wave, for sure) in certain phenomena, while in certain other phenomena it behaves like a particle (it is a photon, a particle of light, for sure). A phenomenon like the interference of light can only be explained thinking of light as a wave. On the other hand, a phenomenon like the photoelectric effect can only be explained when we consider light as particles – photons – which carry not only energy, but also momentum. Bearing in mind that classically we define the momentum of a particle as the product of its mass times its velocity, photons – though massless (i.e., zero mass) are particles that have definite (non zero) momentum! This is something that we cannot quite understand. We could only vaguely describe a photon as some kind of particle without mass, being pure “packets of energy” (but remember, it has momentum, too!). The only way out for physicists confronted with this conundrum has been to consider light as both wave and particle at the same time. Or, in the jargon of the ‘experts,’ light has a dual nature, the wave-particle duality.

Now, consider how fitting this is when Jesus describes Himself as the Light of the world. He is the only One in the whole universe that bears in His personhood the dual nature: the divine nature (He was, is, and always will be God) and the human nature (He became flesh, taking upon Himself humanity). Jesus dying on the cross was fully human; Jesus on the Mount of Transfiguration was fully divine. Theologically we understand the dual nature of Jesus as a necessary condition for the plan of salvation: because the “wages of sin is death” (Romans 6:23), Jesus had to be fully divine to be our Savior (to be able to give us life again) and at the same time He had to be fully human (to be able to be our Substitute, to die in our stead, as a ransom for our life).

In nature, there are many different types of waves: some visible, like water waves that can be seen on the seashore; some invisible, like the sound waves we hear from a radio. Technically, a wave can be loosely defined as an oscillation (or even some perturbation) that travels through space (with or without matter), transferring energy from one place to another. Particles, on the other hand, are understood in physics as (almost) dimensionless localized bodies or objects to which certain qualities or properties (physical, chemical, etc.) such as mass, spin, charge, etc., may be attributed. Light has these two characteristics intrinsically: it is an electromagnetic wave and a particle at the same time. The divine nature of Jesus Christ could be compared to the wave-like nature of the physical light, because He left the glorious courts of Heaven and came to Earth to carry with Him life to bestow on us. His human nature, on the other hand, could be compared to the particle-like nature of light, because when He took humanity upon Himself, He became localized in space, having become a physical body.

We also learn in high school physics classes that light is the only wave (electromagnetic wave) that can travel through empty space (without a matter medium). In other words, light of the remotest corners of the universe can reach us because it penetrates through even the almost perfect vacuum and darkness that exists between galaxies. In the same manner, the light of Jesus can penetrate even the emptiness and darkness of death to bring us back into life. No matter how far out we may have distanced ourselves from the Source of Light, still its saving rays may reach, heal, and save us. How marvelous, gracious, and merciful is our God and Savior, the Light of the world!


Alfredo Suzuki, PhD
Associate Professor of Physics, La Sierra University

Posted in Biblical and Theological Perspectives, Physics | Tagged , , , , , , , , , , | 1 Comment

A Journey of Faith and Science

Toward the end of my graduate studies in organic chemistry at the University of California, Irvine, the conflict that sometimes arises between science and faith presented itself forcibly to me. The closest friend that I had in a group of about 25 people was a brilliant post-doctoral fellow from Georgia, and we decided to take a day trip to the San Diego Zoo to get away from the pressures of the University. At the end of the day as we were headed north to Orange County, he began to speak about the okapi, a giraffe-like animal with stripes on its hind legs reminiscent of a zebra, that we had seen at the zoo.
My friend was speculating on the evolution of this unique animal and its giraffe “cousin”, and he detected a certain reticence from me. He immediately drew the correct conclusion, and questioned with great surprise, “You don’t believe in evolution, do you?” To say that he was surprised would probably be an understatement. More like flabbergasted. We had been friends for more than two years at that point, and I had apparently hidden my insanity well. How could any rational and intelligent person NOT believe in evolution? From this point there was a tension between us, until he left UCI to take a job in the pharmaceutical industry. We have not spoken in more than 10 years, though I have tried to call his cell phone a few times over the years. I believe, though I am not certain, that this episode informed his decision not to maintain our friendship. My friend’s shocked response to my faith in Creation speaks volumes regarding the perception of Darwinian evolution as undeniable and established fact, as opposed to a theory that can be legitimately challenged. A denial of Darwinian orthodoxy is often viewed by its advocates in much the same light as a denial of orthodoxy by any other religious person.

In the intervening years, science and faith have continued to play an important role in my life and I now teach medicinal chemistry and pharmacology at the Loma Linda University School of Pharmacy. As opportunity presents itself, I try to explain to my students the ways in which complex and interdependent biochemical transformations, such as DNA synthesis, defy an evolutionary stepwise origin and demand a Creator. I also try to explain to them why it matters that a Christian should believe that God is the Creator of life, as opposed to creation by the purposeless mutation/adaptation model espoused by the neo-Darwinian synthesis of evolution. And I try to show them how understanding their job as pharmacists allows them to minister to their patients, and in their own way to heal as Jesus would were He in their place.

My research is focused on aggressive and difficult-to-treat cancers, and I hope that these studies might eventually lead to therapies that can improve cancer patients’ lives. I’ve found that though the conflict between faith and science may occasionally strain friendships, and has strained several of mine over the years, there is no logical tension between the two. It is entirely possible to be a Bible-believing (yes, even those early chapters in Genesis), Jesus-loving Christian and a believer and practitioner of science.

The Bible describes us as “fearfully and wonderfully made” (Psalm 139:14). It says that we are the product of careful thought and preparation, and created in the image of a God that loves us (Genesis 1 and 2). These same things are true of the world around us, the study of which we call “science.” My favorite author, Ellen White, says that “All truths, whether in nature or Revelation, agree.” (Signs of the Times, 1884, #11). The honest pursuit of truth should never cause Christians to fear that their faith will be shaken or lost. We may not be able to understand everything that is found in nature, but the reality is that no one does. But the truth can only be found in the One who calls Himself “the Way, the Truth, and the Life” (John 14:6). In my experience, science rightly understood leads us closer to the Author of all knowledge and provides for a greater appreciation for the work of His hands.

Understanding the world in which we live through the study of science in its various forms is a gift that God offers to His children. Reading the Scriptures to learn where this world came from, why we are here and where we are going is another gift the Lord has generously provided. The love of God for His children is revealed in both science and Revelation, and the blessing of God rests upon all those that seek Him through all of the means that He has provided. “Ye shall seek Me, and find Me, when ye shall search for Me with all your heart” (Jeremiah 29:13).


Kristopher E. Boyle, PhD
Assistant Professor of Medicinal Chemistry
Loma Linda University

Posted in Profiles of Christian Scientists | Tagged , , | 2 Comments

A review of the nature documentary “The Riot and the Dance”

This movie premiered in US movie theaters on March 19, 2018, followed by a nationwide theatrical encore on April 19th. It is not yet available on DVD. More information and additional resources about the documentary can be found at http://riotandthedance.com and https://www.facebook.com/riotandthedance/


A flyer advertising the release of the movie

Most nature documentaries include some language that refers to an underlying naturalistic understanding of origins. They convey the idea that the deeply textured behaviors and interactions of the biological world emerged from impersonal physical necessities and a really long chain of purposeless chance events. However, the recently released nature documentary “The Riot and the Dance” breaks this common pattern in a refreshing way. Instead of suppressing the undeniable richness of meaning in nature, this film embraces with beautiful consistency a simple premise from its very start: God is the Maker of all there is and we resonate with other living beings because we all are the expression of His design and creativity. This bold choice sets this movie apart from classic nature documentaries and provides the foundation for the exploration of different habitats and their inhabitants. In speaking of other creatures, biologist Gordon Wilson, the narrating voice of the film, invites us to “see them truly as gifts, as miracles.” With reference to the redwood forests of the Pacific NW of the US, he remarks: “God has been using starlight to craft wooden towers older than the modern world. If He spared 2,000 years to shape something, can we spare the time to give it a glance?” In a moment of rare lyrical intensity, Wilson comments on a close up shot of a wild puma saying: “Look a puma in the face: really look. Know that its symmetry and grace was invented from nothing. Who can do such a thing? Only your Father.” What a joy to hear this kind of language punctuating quality videography of different aspects of the creation.

Openly embracing a theistic explanation for the origin of our world and the life that thrives in it has three direct consequences, clearly demonstrated in the movie: 1) First, it encourages wonder in the observer, because living creatures are received as works of art rather than machinery assembled by evolutionary engineering. This way of doing biology is not scared of poetry, and seeks to transcend the mere observation of the constitutive components of reality to spring into an act of celebration; 2) Second, it establishes a strong sense of responsibility founded on the traditional Christian understanding of creation, where humans are called to be keepers of this world. In Wilson’s words, “God has given us dominion and we have to take that charge very seriously.” The movie models an excellent example of how this responsibility requires mindful participation and continuous interrogation and can be fulfilled with playfulness and innocence rather than greed or disinterest; 3) Thirdly, it forces us to acknowledge the existence of tension and dissonance in the natural order when compared to the divine ideal revealed in the Scriptures. Nature is not only the source of thrilling wonder but also of perplexing realities not easily accounted for. This ambiguity is exactly what the title of the film, “The Riot and the Dance,” intends to convey. Something in the creation is not as it should be and we are puzzled by it, although we cannot mistake its evil nature.

The narrative trajectory of the movie starts with a brief opening section where Wilson introduces himself, and continues with a journey of exploration of different habitats and animals, covering local (US) and exotic (Sri Lanka) examples. A concluding section focuses on snakes, a common icon of natural evil, and after the closing credits there is an extensive appendix of interviews with Wilson and the film director (Wilson’s nephew), Ken Ham of Answers in Genesis, author Eric Metaxas, and Christian hip hop artist Propaganda. The major themes addressed throughout the movie are exploration and enjoyment of nature, environmental stewardship, and natural evil. I really liked that the nature sequences in the film are interjected by brief segments where Wilson speaks directly to the camera to introduce the discussion of those themes. However, some of the transitions between different habitats felt a bit disconnected, not always contributing to the construction of a compelling overarching story. The quality of the images and the spectrum of animal behaviors portrayed was very good. For me, some of the most impressive shots were close-ups of the scales of several reptiles caught by Wilson, showing beautiful coloration patterns. The high resolution shots zooming in on the geometric arrangement of the scales covering the skin of these animals certainly made me think of them as incredible living masterpieces. The closing interviews segment of the documentary helped to understand some of the history behind the making of the film, but was very different in style and made the movie perhaps too long. This did not leave the same flavor in our palate that had been constructed in the beautiful movie proper.

When it comes to the deeper reflections elicited by the film, I can think of two aspects that I would like to discuss more with Wilson to understand further his wisdom and perspective. The first is the possibility that heightened appreciation for the creation could translate into a sort of “nature worship.” If evolution has no place for intelligent design in nature, at the opposite side of the spectrum is a world where every minute detail is assigned incomparable value. Could this result in a posture towards the creation that is almost afraid of interaction and engagement for fear of disrupting a divinely ordained balance? To be fair, Wilson does not fall into this trap and projects a well-centered understanding of human rulership that is gentle and passionate, but not at all passive.

Director Andy Wilson explains in the final interview how he wanted to avoid the approach of other documentaries that “treat the animals as if they are sacred: the animals must not be touched, the animals take precedence over mankind.” However, in a scene where Wilson is crossing a river, we see him let a land leech crawl up his leg and draw a good sip of blood while he comments “Behold, God and I provide.” At times, I wonder if rather than turning back to God for all we observe in this world we should be impressed by how bad things have gone and read among the lines of nature the story of a cosmic conflict, elements of which we need to call out for what they are: not good. And again, Wilson seems to capture this tension by oscillating between the poles of wonder and appreciation but also statements affirming that “this is not how the world was meant to be, this is the result of the fall. It is more riot than it is dance.” However, he also appears to embrace the world as it is: “How much of this world does God love? How much has He given to us? The answer is the same: all of it. Every prickle and every pebble, every storm and every breeze, every insect and every lizard.” There is something tragic in the scene where a crested serpent eagle engages in an extenuating fight to kill a land monitor, but geckos preying on termites are apparently ok: God “makes them desperately want what He has already arranged to give them. Feast little lizards.” Maybe this tension is indeed where we should situate ourselves as Christian scientists in reading the message of the world around us.

The second aspect, connected to the first, is the stated desire to bring into the fold of this movie the narration of “Christian evolutionists.” Director Andy Wilson offers that “all of us should be able to look at the world and love what God gave us. Part of the goal of the film was not to have a debate movie where Christians fought with each other, but a film to celebrate what we all agree God gave us and then have some intermural debate about how He gave that to us.” But are animal death and predation part of “what we all agree God gave us?” If God uses natural selection to play His music, one would look at the hardships of animal life in a reverent rather than contrite and troubled way. But Wilson does promote throughout the movie the concept of the fall and the curse, and not only a spiritual one, but one that materially affected the biological world. He goes as far as to explicitly connect all the biological suffering to the results of our human choice: “Predator-prey, parasite-host, all these things are the result of the fall. The creation needs redemption.” “When man fell, so did the world, now death is something that we all share.” “Everything here is groaning against death because of our fall.” Therefore, it would be interesting to see how he sees that this approach can square with the perspective of a “Christian evolutionist.”

I was very grateful for and resonated with the perspective adopted in this movie. It is encouraging to see that new quality documentaries are being produced that embrace a language and a worldview in which many of us breathe and move. This film also provides a great opportunity to invite a skeptic friend to engage with a different way of looking at nature, that is genuine, honest, and joyous. I am looking forward to the release of the next episode of “The Riot and the Dance,” which will feature aquatic creatures!


Ronny Nalin, PhD
Associate Scientist
Geoscience Research Institute

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DNA and Design

Imagine walking down the beach and coming across the words “Romeo loves Juliet” written in the sand. Most of us have experienced something like this and would not be surprised, but most people would be surprised to find the entire text of William Shakespeare’s play Romeo and Juliet written in sand. Why is this? The obvious reason is that sand is the wrong material for large writing projects. Sand grains move about easily and text written in it is quickly obliterated (Figure 1). Before the first act was completely written in sand, the beginning may be gone if the wind is blowing or waves wash over it.

beach-949536_960_720

Figure 1: Sand on a beach can be a romantic but not highly efficient information storage system.

On the other hand, it is not surprising to find Romeo and Juliet written out on paper. Because it is compact and lasts for many years, paper is an excellent material for storing information. We could write information on other materials – over the course of history, humans have employed everything from rocks to parchment made from sheep skins as information storage media – but cheap abundant long-lasting paper has proven to be one of the best media ever invented for storing information.

DNA – The stable genetic information storage medium

Inside cells, we find an information storage medium that, like paper, appears to be just the right medium for the information it stores; we call it Deoxyribonucleic Acid or DNA. One reason DNA is an excellent storage medium for genetic data is its amazing chemical stability. DNA can last for thousands of years after an organism has died, and this has allowed us to read the DNA of long extinct organisms ranging from our Neanderthal relatives[1] to woolly mammoths.[2] Chemical stability is essential to the function of DNA. If it were unstable, the information that it encodes would be quickly degraded, like information written in sand.

DNA – An efficient storage medium

Our own DNA illustrates another essential attribute of DNA. The human genome comprises all our DNA packaged into the 23 human chromosomes, two copies of which are found in most cells,[3] as well as DNA within mitochondria. DNA stores information far more efficiently than printed words on paper. For example, human mitochondrial DNA is only about 5.6 μm long–about one hundredth the diameter of a typical period at the end of a sentence–but printed out as letters on paper, its DNA sequence takes up about 6 pages. Similarly, the entire human genome is about a meter long but requires around a million pages to print out! Clearly a million pages will not fit inside a cell, but all that information will fit inside the tiny nucleus of a cell if it is encoded in DNA. The ability of DNA to store information in a tiny space makes it the most efficient known information storage medium in terms of information density.

DNA – An accurately copied medium

The double helical structure of DNA also contributes in an amazing way to its function as an information storage medium. When most cells divide, it is necessary to make a complete copy of the DNA in the “mother” cell so that each “daughter” cell gets one complete copy of the mother cell’s DNA. Information is encoded in DNA using sequences of chemicals called nucleotide bases. These bases are analogous to the letters we use to spell out information and a complete copy of the human genome contains about 3 billion of them. When human cells divide, the challenge is to accurately copy 6 billion bases because each mother cell contains two copies of the human genome.

Humans start out as a single fertilized egg cell, which divides until a person reaches the adult number of cells, which is around 37 trillion.[4] As adults, our cells continue to divide and grow as we lose old cells, so millions of cells in our bodies divide every day and thus millions of copies of the 6 billion bases in each cell’s DNA must be accurately made. While the number of DNA replications and the 3 billion base length of the human genome may seem impressive, this is not exceptional. Many other organisms, ranging from maize to some salamanders, have significantly larger genomes. The largest animal genome reported is for the marbled lungfish, Protopterus aethiopicus, with 139 billion bases in its genome, but organisms with even larger genomes are known.[5]

When James Watson and Francis Crick published their seminal 1953 paper[6] revealing the double helical structure of DNA to the world, they immediately noted that the structure suggests a mechanism for accurate DNA replication:

It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.

dna helix

Figure 2: The structure of the DNA double helix. Image courtesy of Zephyris (CC BY-SA 3.0).

The pairing Watson and Crick are referring to involves the chemical base “letters” of the DNA alphabet already mentioned. These flat molecules are attached to the two strands of the double helix. As the two strands of the double helix wind around each other, the bases point into the center and interact with one another in very specific ways. One class of bases, the purine bases Adenine (A) and Guanine (G), is relatively large; while the other class, the pyrimidine bases Thymine (T) and Cytosine (C), are smaller. In addition, charges on the surface of these bases are distributed differently. Because of this and the geometry of DNA with the bases pointing toward each other, Adenine (A) on one strand of the double helix always pairs up with Thymine (T) on the opposite strand and vice versa. The same is true for Guanine (G) and Cytosine (C). Thus, if you have an A on one strand of the double helix, you can know that there is a T on the opposite strand, and if you have a C on one strand, you can know that there is G on the opposite strand.

If the double helix is unzipped to make individual strands of DNA, each strand contains a negative copy of the opposite strand. When DNA is replicated, the DNA double helix is unzipped and each strand serves as the template for making an exact copy of the other strand. Obviously there is complex cellular machinery that makes this happen, but if one strand has the sequence AGTCCGC, then the opposite strand can be reconstructed exactly from it as TCAGGCG.[7] Thus it is that the structure of DNA contributes to the amazing way it can be replicated with almost inconceivable speed and accuracy.

The origin of DNA as the genetic material of organisms

The more we learn about DNA, the better suited it appears to its role as an information storage medium inside cells. We have talked about three ideal characteristics that it exhibits: 1) It is chemically stable and thus does not rapidly degrade the information stored in it, 2) DNA is amazingly information dense, storing massive quantities of information in an incredibly small volume; 3) The structure of DNA contributes to its ability to be accurately copied at amazing speed, which is necessary when cells are dividing to make new cells. There are other characteristics that DNA exhibits that make it ideal, but discussing them gets progressively more technical and these three are sufficient to illustrate the point. There may be some other materials that could do some of what DNA does, but none are known that fulfill all the requirements of a genetic material as well as DNA does.

This raises the question of how organisms ended up using DNA rather than some inferior molecule to store genetic information. For the open-minded there are at least two possibilities, either DNA was chosen as the genetic material by someone who knew what they were doing, or DNA was chosen as the genetic material by something that didn’t know what it was doing. The latter position is the materialistic belief of Darwinism. How might this have worked? Given the amazing fit between the properties of DNA and its function, and the diverse molecules made by organisms, it is hard to imagine nature arrived at this solution on its first attempt. Something had to be the initial genetic material and then various other solutions to the need for a genetic material were tried until natural selection settled on the essentially ideal solution of DNA.

There is a significant problem with this Darwinian scenario. Darwin pointed out that for his mechanism to work, it must proceed by “by numerous, successive, slight modifications.”[8] However, changing genetic materials, even with relatively small changes to the chemicals involved, is not possibly a slight modification from the perspective of the organism. An analogy might be trying to swap out the hard disk of a computer for paper, or information chiseled into rock. Information is stored in the form of different magnetic states on hard drives, the equipment to retrieve that information must match the medium it is stored in. Thus, the heads that read changes in magnetic state on a hard disk are incapable of reading ink on paper or letters carved into stone. The same is true of the equipment used by cells to read information from the genetic material of cells. Today we can study the machinery found inside cells and see that we can’t substitute a different kind of molecule for DNA. Molecules like polysaccharides, triglycerides or proteins – all of which are naturally made inside cells – are not particularly good information storage media, but even if they were, they are not read by the machinery that reads DNA.

We can also see that devices capable of reading different media are a complex engineering challenge, but creating a device flexible enough to read multiple media is orders of magnitude more difficult. This is why when the transition was made from optical drives to USB drives no attempt was made to create systems that read both; they are read by different devices inside computers. To go with the materialistic scenario involving multiple genetic materials, one needs mechanisms for reading the stored information in different media that somehow anticipate the need to read it before it is being used. In reality, switching genetic materials, even switching between fairly closely related chemicals, requires a coordinated change in several molecular machines inside cells, something that seems quite remarkable in any system, let alone a system that is unguided in any way.

The alternative theory, that DNA was chosen as the genetic material by someone who knew what they were doing, can be compared with our normal experience. One of the first things engineers look at when presented with an engineering problem is the materials available and a decision is made about which materials will best serve the purposes of the problem they seek to address. For example, when designing a car engine, an engineer needs to use materials that can withstand the heat and mechanical strain inside the engine. Water is not the right material for an engine block, neither is wood or concrete; certain metals work very well for this purpose, so these metals are the materials most commonly used. Engineers know the specifications of the project being worked on and the specifications of the materials available. They then match the material exhibiting the necessary specifications with the project at hand. This observation fits well with our understanding of DNA as the genetic material; it is well explained within the paradigm of a wise Designer who chose an ideal material for the purpose of storing genetic information within the organisms He created. Satisfied with this choice, and many others, He could thus pronounce at the completion of His creation that it was “very good.”[9]

There is clearly an argument to be made for design in living things based on the choice of DNA as the genetic material, but what about the information encoded in DNA? Christians believe God created living things and is the ultimate source of information in genomes. In contrast, the most common alternative theory of origins–materialistic Darwinism–attributes genomic information to chance mutations and natural laws, particularly natural selection. Let’s look at two attributes of genomes that shed light on their origin and ultimately the origin of life.

Is much of the information coded in DNA actually junk?

Our understanding of genomes was held back by the rush to declare most of many genomes “junk.”[10] Susumu Ohno, who coined the term “junk DNA,” elegantly expressed this Darwinian viewpoint:

“[T]he earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?”[11]

Much DNA does not code for proteins, and many biologists initially assumed that these non-coding DNA sequences therefore lacked function.  The logic boiled down to, “if we don’t know what it does, it must do nothing.”  However, much data now demonstrate that this logic leads to a false conclusion: non-coding DNA often exhibits important functions. This understanding has revolutionized how biologists view genomes. Instead of vast deserts with occasional oases of functional information, genomes now seem more like rainforests of information with a dazzling array of genes, control mechanisms and logic circuits.

Genes are smarter than we thought

According to the “one gene, one enzyme” model proposed by Beadle and Tatum (for which they won a Nobel Prize), each gene codes for a single protein; but now everything has changed. Current estimates indicate that humans have less than 25,000 genes, but produce more than 100,000 proteins;[12] thus at least some genes must be capable of producing multiple proteins.

2LKX_screenshot

Figure 3: NMR structure of the homeodomain of Pitx2 in complex with a TAATCC DNA binding site. PDB ID: 2LKX [Chaney, B.A., Clark-Baldwin, K., Dave, V., Ma, J., Rance, M. (2005). Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome. Biochemistry 44: 7497-7511.] Rendered using NGL viewer [AS Rose and PW Hildebrand. NGL Viewer: a web application for molecular visualization. Nucl Acids Res (1 July 2015) 43 (W1): W576-W579 first published online April 29, 2015. doi:10.1093/nar/gkv402].

How is this achieved? Let’s illustrate with the human Paired-like homeodomain transcription factor 2 gene (also called Pituitary Homeobox 2 and abbreviated Pitx2), which shows how RNA processing creates several different proteins from one gene. The PITX2 protein (Figure 3) plays a role in development of the head and eyes, among other things.[13] Pitx2 includes six segments called exons that code for parts of the protein. These are separated by five introns. When the DNA coding this gene is copied to RNA for use by the cell’s protein manufacturing machinery, it can be processed in different ways to code for different proteins. By joining exons 1, 2, 5 and 6, mRNA for a version of PITX2 called “Isoform A”, or PITX2A is made. Joining exons 1,2,3,5 and 6 makes mRNA for PITX2B and exons 4, 5 and 6 form the mRNA for PITX2C. Other mechanisms make even more forms of PITX2.[14] Cells need to make the right “version” of PITX2 in the right place at the right time if the organism they are part of is to develop normally.

How does the cell “know” when to make one form of a protein but not others? This brings us back to some of what was once dismissed as “junk” DNA and indicates why genomes are now understood to be far more dynamic than initially imagined. The complex systems controlling exon splicing appear to involve sequences occupying at least one third of the human genome,[15] far exceeding the 3 % of the human genome thought to be functional a few years ago. The picture of DNA that is emerging shows it does in fact store vast quantities of information, much of which was missed by the first scientists to study it. Much more is probably yet to be discovered.

Conclusions

There is beauty, complexity, elegance and efficiency in the choice of DNA as the medium for storing genetic information, and the information itself is amazing. Some of what we know about genomes fits well with the thesis of common ancestry and Darwinian evolution, but when taken as a whole, the evidence is more consistent with the Biblical worldview in which a Designer, God, accounts for the choice of DNA as the genetic material, the enormous quantities of information stored in it and the elegant arrangement of that information in genomes.

When the Creator God wrote the 10 Commandments,[16] He did so in the durable medium of stone; but when He wrote the sins of the self-righteous scribes and Pharisees, He wrote in dust, where His words would be quickly obliterated.[17] The God of the Bible demonstrated His ability to choose appropriate media in which to record information, it should not be surprising to find that in living things He chose a medium as well suited to the task of recording genetic information as DNA, or that the information stored in DNA is elegant and amazing. Every person, every creature, every plant–indeed every living organism–is an exquisite repository of genetic information encoded in DNA, information far more exquisite and deeply meaningful than anything written by William Shakespeare or any other human author. Christians have good reason to believe that we are “fearfully and wonderfully made”[18] and that God, who created us along with all other things, is worthy of our worship.

References

[1] Green RE, Krause J, Briggs AW, et al. 2010. A Draft Sequence of the Neandertal Genome. Science 328(5979):710-722. DOI: 10.1126/science.1188021

[2] Miller W, Drautz DI, Ratan A, et al. 2008. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456:387-390. doi:10.1038/nature07446

[3] We get a complete set of human chromosomes from each parent; 23 from our mother and 23 from our father for a total of 46. Most human cells carry all 46 chromosomes in their nucleus.

[4] Bianconi E, Piovesan A, Facchin F, Beraudi A, Casadei R, Frabetti F, Vitale L, Pelleri MC, Tassani S, Piva F, Perez-Amodio S, Strippoli P, Canaider S. 2013. An estimation of the number of cells in the human body. Annals of Human Biology. 40(6):463-71. doi: 10.3109/03014460.2013.807878.

[5] Pellicer J, Fay MF, Leitch AJ. 2010. The largest eukaryotic genome of them all? Botanical Journal of the Linnean Society 164(1):10–15. DOI: 10.1111/j.1095-8339.2010.01072.x

[6] Watson JD, Crick FHC. 1953. A structure for deoxyribose nucleic acid. Nature 171:737-738.

[7] Note that because of the conventions usually used by molecular biologists, these sequences would not be written exactly like this.

[8] Darwin, C. R. 1859. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. London: John Murray. 1st edition, 1st issue. P 189.

[9] Genesis 1:31

[10] Makalowski, W. 2003. Not junk after all. Science 300:5623.

[11] Ohno S. 1972. So much “junk” DNA in our genome. Brookhaven symposia in biology. P. 366-70 in Evolution of genetic systems (H. H. Smith, ed.). Gordon and Breach, New York.

[12] Clamp, M., B. Fry, M. Kamal, X. Xie, J. Cuff, M. F. Lin, M. Kellis, K. Lindblad-Toh, and E. S. Lander. 2007. Distinguishing protein-coding and noncoding genes in the human genome. Proceedings of the National Academy of Sciences USA 104:19428–19433.

[13] Gage PJ, Suh H, Camper SA. 1999. The bicoid-related Pitx gene family in development. Mammalian Genome 10:197-200.

[14] Lamba, P., T. A. Hjalt, and D. J. Bernard. 2008. Novel forms of Paired-like homeodomain transcription factor 2 (PITX2): Generation by alternative translation initiation and mRNA splicing. BMC Molecular Biology 9:31.

[15] Zhang, C., W.-H. Li, A. R. Krainer, and M. Q. Zhang. 2008. RNA landscape of evolution for optimal exon and intron discrimination. Proceedings of the National Academy of Sciences USA 105:5797–5802.

[16] Exodus 31:18, Deuteronomy 9:10

[17] John 8:7,8

[18] Psalm 139:14


Timothy G. Standish, PhD
Senior Scientist, Geoscience Research Institute

A former version of this article was published in German on the magazine Info Vero

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