Where Science and Faith Converge
  • Can Keratin in Feathers Survive for Millions of Years?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Aug 10, 2016

    I don’t like conflict. In fact, I try to avoid it whenever possible. And that’s part of the reason I never wanted to become directly involved in the young-earth/old-earth controversy that takes place within the church.

    Frankly, I find the debate tedious, and a distraction from the real work at hand: helping skeptics and seekers recognize the scientific evidence for God’s existence and Scripture’s reliability.

    Of course, if people ask me age-of-the-earth questions, I am quick to explain why I hold to an old-earth/day-age interpretation for Genesis 1 and what I see as biblical, theological, and scientific issues with a young-earth/calendar day interpretation of the Genesis 1 creation account.

    Soft Tissues in Fossils and the Age of the Earth

    Over the course of the last few years, one question that has come up a lot relates to the discovery of soft tissue remnants in fossils, such as the blood cells and blood vessels remains recovered from a T. rex specimen that age-dates to 68 million years old. Young earth creationists make use of these surprising results to argue that it is impossible for fossils to be millions of years old. They argue that soft tissues shouldn’t survive that long. These materials should readily degrade in a few thousand years. In their view, these finds challenge the reliability of radiometric dating methods used to determine the age of these fossils, and along with it, Earth’s antiquity. Instead, they argue that these breakthrough discoveries provide compelling scientific evidence for a young Earth and support the idea that the fossil record results from a recent global (worldwide) flood.

    Because I’m a biochemist—and an old earth creationist—people frequently ask me how I make sense of the T. rex find and the discovery of other types of soft tissue remnants in the fossil remains of other creatures that age-date to several hundred million years, in some cases.

    Dinosaur Blood and the Age of the Earth

    These queries eventually motivated me to write Dinosaur Blood and the Age of the Earth. And I am glad I did. Aside from the young-earth/old-earth debate, the scientific questions related to soft tissue finds in fossils are captivating.

    The central question of Dinosaur Blood and the Age of the Earth centers around soft tissue durability: If radiometric dating is reliable, then how is it possible for soft tissue remnants to persist for millions of years?

    Recent work by a research team at North Carolina State University (NC State)—headed up by Mary Schweitzer—helps address this question, specifically focusing on beta-keratin fragments recovered from the fossilized feathers and claws of Shuvuuia deserti and Rahonavis ostromi.1

    How Can Keratin Survive in Fossils?

    As I discuss in Dinosaur Blood and the Age of the Earth, some biomolecules (such as keratins) form extremely stable structures that delay their degradation. Keratins have a number of structural features (such as extensive crosslinking) that helps explain why fragments of these proteins could survive for tens of millions of years, under the right conditions.2 But my analysis was theoretical. Even though my assessment was based on sound biochemical principles, it would be nice to have some corroborating experimental evidence to support my claims. (The old saying in science applies: “theories guide, experiments decide.”) And that is precisely what the NC State researchers provide in their recent study.

    Feather Decomposition

    Schweitzer and her team conducted a ten-year experiment to gain insight into the natural degradation processes of feathers (and other biological materials made up of keratins such as skin, claws, beaks, and hair). To do this, they exposed feathers from a Hungarian partridge to a variety of conditions, and then analyzed the samples busing: (1) transmission electron microscopy (TEM) to monitor changes in the fine structure of the feather’s anatomy; and (2) a technique called in situ immunofluorescence to determine if pieces of keratin proteins persisted in the feather remains.

    Of particular interest is the feather samples Schweitzer and her team wrapped in aluminum foil and heated in an oven for 10 years at 630°F—conditions used to sterilize glassware. Many paleontologists consider high heat to be a proxy for deep time.

    Perhaps it is no surprise, when viewed under a microscope, the macroscopic features of feathers treated at high temperatures were completely lost. Instead the only thing visible were shiny black pieces of “charcoal-like” material. Yet, when examined at high magnification with a TEM, the investigators were able to visualize fragments of feather barbs. Using their immunofluorescence technique, the researchers were able to detect clear evidence of keratin fragments in the sample.

    These observations align with my thoughts about keratin’s durability, making it all the more reasonable to think that soft tissue remnants persist in millions-of-years old fossil remains. In fact, when the researchers applied their immunofluorescence to the Shuvuuia deserti samples, once again, they found evidence for keratin fragments in these fossil remains.

    Preservation Mechanisms

    As I point out in Dinosaur Blood and the Age of the Earth, molecular durability alone isn’t sufficient to account for soft tissue survivability. For soft tissue remnants to persist in fossil, the rate of fossilization has to outpace the rate of soft tissue degradation. When that happens, a mineral ‘casing’ will entomb the soft tissue before it completely decomposes, preserving it for paleontologists to later discover. In addition to molecular durability, scientists have identified a number of mechanisms that contribute to both the degradation and preservation of soft tissues during the process of burial and fossilization.

    Along these lines, the NC State scientists speculate on processes that might extend keratin’s survivability in feathers—at least, long enough for mineral entombment to occur. They think one of their observations about the high-heat sample offers a clue. The research team noted that melanosomes (the organelles that harbor pigments, giving feathers their colors) were absent after heating for ten years at 630°F. On this basis, they conclude that paleontologists have made a mistake when they interpret microbodies as melanosomes in fossilized feathers. Instead, they think that the mirobodies derive from microbes.

    This reinterpretation is good news for keratin preservation on two accounts. It is true that microbial activity can destroy soft tissues, but the NC State scientists think it can also help speed up the fossilization process leading to the preservation of keratin remnants. How? Because microbes secrete materials (called exopolymeric substances) that promote deposition of minerals, speeding up the entombment of the soft tissue. Additionally, the NC State researchers think that melanosome degradation may also be important. When these organelles break down, they release their contents (eumelanin) which may function like a fixative, slowing down tissue degradation long enough for the soft tissue to be entombed.

    The NC State study has unearthed fascinating details regarding feather decomposition and provides key insights that help account for the persistence of keratin in fossilized remains of reptiles, birds, and feathered dinosaurs that date to tens of millions of years old.

    Resources
    Structure of Collagen Unravels the Case for a Young Earth” by Fazale Rana (Article)
    Dinosaur Blood and the Age of the Earth by Fazale Rana (Book)

    Endnotes
    1. Alison Moyer, Wenxia Zheng, and Mary Schweitzer, “Keratin Durability Has Implications for the Fossil Record: Results from a 10 Year Feather Degradation Experiment,” PLoS One 11 (July 2016): e0157699, doi:10.1371/journal.pone.0157699.
    2. Fazale Rana, Dinosaur Blood and the Age of the Earth (Covina, CA: RTB Press, 2016), 57–58.
  • The Evolution of the Automobile: Evidence for Intelligent Design

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Aug 03, 2016

    “It’s déjà vu all over again.”

    As the story goes, baseball player and manager Yogi Berra first uttered this famous yogi-ism sitting in the dugout watching Mickey Mantle and Roger Maris hit back-to-back home runs. Something that happened on more than one occasion.

    Yogi Berra’s verbal blunders are legendary. But, perhaps none top the blunder made by biologist Tim Berra. Berra’s blunder didn’t have anything to do with what he said, but with what he wrote in his book Evolution and the Myth of Creationism, published in 1990.

    Berra’s Blunder

    Targeting a nontechnical audience, Berra presented a case for biological evolution and explained why he and so many scientists think evolution is a fact. As part of this project, he described the evidence for human evolution, highlighting the progressive features of the hominid fossil record. Berra argues,

    “If the australopithecines, Homo habilis, and Homo erectus were alive today, and if we could parade them before the world, there could be no doubt about our relatedness to them. It would be like attending an auto show. If you look at a 1953 Corvette and compare it to the latest model, only the most general resemblances are evident, but if you compare a 1953 and a 1954 Corvette, side by side, then a 1954 and 1955 model, and so on, the descent with modification is overwhelmingly obvious. This is what paleontologists do with fossils, and the evidence is so solid and comprehensive that it cannot be denied by reasonable people.”1

    In comparing Corvette models with “transitional intermediates” in the fossil record, Berra made a significant error that has become known among creationists and ID proponents as Berra’s blunder. It almost goes without saying, Berra’s mistake was to use Corvettes—machines designed by automotive engineers—as an analogy for the hominid fossil record, claiming that sequential anatomical changes among the various hominid species reflect the outworking of an unguided evolutionary process in the same way that sequential design changes to Corvettes reflect the evolution of technology. But, as pointed out at that time by several creationists and intelligent design proponents, the Corvette sequence actually tells us something about how intelligent agents sometimes create: namely, designers can attain their goals by progressively modifying existing designs. To put it another way, the chronological appearance of organisms in the fossil record displaying serial changes to their anatomical, physiological, and behavioral features could be explained as the work of a Creator who was successively producing creatures that displayed modifications of an archetypical design. In this sense, the fossil record doesn’t necessarily compel reasonable people to accept biological evolution any more than does the evolution of the American automobile.

    The sequential changes seen in the fossil record just as reasonably reflect the work of a mind as mechanism.

    Déjà Vu Once More

    Recently, researchers from UCLA made the same blunder as Tim Berra—all over again!2 These investigators wanted to understand the principles that influence the tempo and mode for technology development in a society. As a case study, these investigators examined the appearance and disappearance of American car and truck models manufactured between 1896 (when automobiles were first produced) and 2014, using the same approach that paleontologists might use to study the fossil record. Specifically, they monitored the year-by-year diversity of automobile models, paying special attention to the number of new models that were produced (analogous to speciation) each year and the number of discontinued models (analogous to extinction).

    These researchers also explored the factors influencing the diversity of automobile models each year. Particularly, they assessed the effects of competition, and the impact of Gross Domestic Product (GDP) and oil prices.

    Their analysis indicates that the “origination” and “extinction” rates of automobile models displayed highly similar patterns over the course of the last 118 years. In both cases, origination and extinction rates were highest early in the automobile’s history, gradually declining to lower rates over time. The rates of decline dramatically slowed in the 1960s when the Big Three auto manufacturers rose to dominance in the American market place. Since the 1980s, the rate of automobile model extinction has outpaced the appearance rate of new models. However, during this time frame, the lifespan of automobile models has significantly increased.

    The UCLA researchers also discovered that completion has had a much greater influence on automobile diversity than GDP and oil prices.

    Based on these results, the authors of this study argue that when a technology is in its early stages, manufacturers introduce more experimental designs into the marketplace. But because these designs are experimental, they also disappear more rapidly. They maintain that the appearance and disappearance rates slow as dominant designs emerge. When that happens, it becomes too costly to introduce experimental models into the marketplace. Eventually, cost becomes such a significant factor that it causes the life expectancy of designs to persist for longer time periods.

    Based on this study, the UCLA scientists predict that in the near future the number of hybrid and electric car designs will rapidly diversify—a radiation event, of sorts—because these technologies are in their nascent stages.

    The Fossil Record and the Case for Creation

    The UCLA researchers demonstrated that some of the techniques paleontologists use to study the fossil record—and hence, the history of life on Earth—can yield important insights about the way cultures and technologies change and develop. However, as with Berra’s blunder, they treated designed objects as if they were fossils, which, according to the evolutionary paradigm, are produced by unguided, mechanistic processes. The approach the UCLA research team used to study technology development, once again, highlights the fact that the sequential changes seen in the fossil record just as reasonably reflect the work of a mind as mechanism.

    But, it is possible to take the implications of their work one step further. Not only can we argue that the progressive anatomical changes observed in fossilized organisms reflect the Creator’s handiwork, but so do overall patterns in the fossil record. The UCLA study demonstrates that when it comes to technology produced by human designers, the number of design variants and the rate that designs appear and disappear from the marketplace have a rational basis. Though the rationale may be different than what the UCLA researchers discovered for the automobile’s evolution, it becomes all the more reasonable to view changes in biological diversity and origination and extinction rates in the fossil record as reflecting a Creator’s intentional activity.

    In other words, the evidence (the fossil record and homology) that biologists insist provides compelling support for the evolutionary paradigm actually finds ready explanation from a creation model perspective.

    Resources

    Archetype or Ancestor? Sir Richard Owen and the Case for Design” by Fazale Rana (Article)

    Endnotes
    1. Tim Berra, Evolution and the Myth of Creationism (Stanford, CA: Stanford University Press, 1990), 117.
    2. Erik Gjesfjeld et al., “Competition and Extinction Explain the Evolution of Diversity in American Automobiles,” Palgrave Communications 2 (May 2016): 16019, doi:10.1057/palcomms.2016.19.
  • Science News Flash: Are Humans Still Evolving?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Aug 01, 2016

    Are human beings divinely created? Or are we the product of an evolutionary history? Or both?

    Nearly everyone has some interest in human origins. And for that reason, it’s not surprising that discoveries in anthropology frequently garner headlines and serve as fodder for popular science pieces.

    Recently, paleoanthropologist John Hawks from the University of Wisconsin-Madison wrote an excellent piece for the August 2016 edition of The Scientist entitled, “Humans Never Stopped Evolving.” In this article, Hawks discusses a number of recent studies that identify natural selection at work in human beings and presents scientific updates on several well-known examples of evolutionary changes in humans, such as the ability to digest milk sugar and the origin of regional differences (racial diversity).

    In all cases, the underlying implication is: If we observe human evolution happening before our eyes—time and time againthen we have clear-cut evidence that human beings evolved. But is that really the case? Is that the proper conclusion to draw from these scientific observations?

    I would say, no.

    From a creationist perspective, that the ability of humans (and other creatures) to adapt through microevolutionary change is evidence for God’s provision and providence.

    The evolutionary changes described by Hawks are merely examples of microevolutionary changes—variation within a species. In fact, it could be argued from a creationist perspective that the ability of humans (and other creatures) to adapt through microevolutionary change is evidence for God’s provision and providence.

    Hawks’ examples of human evolution fall into the same category as (1) the acquisition of antibiotic resistance by bacteria; (2) the development of pesticide and herbicide resistance by insects and plants; (3) the change in wing color of the peppered moth; and (4) the variation in beak shape by the finches on the Galapagos Islands.

    These common examples of evolutionary changes are often cited as evidence for biological evolution. Microevolutionary changes, however, don’t necessarily extend to support macroevolutionary changes (the creation of biological novelty through undirected evolutionary processes). And there are many reasons—see Who Was Adam?—to be skeptical of evolutionary explanations for the origin of humanity.

    Evidence for human microevolution does not constitute evidence for human evolution.

    Resources
    Evidence That Humans Are Evolving Is Not Evidence for Human Evolution” by Fazale Rana (Article)
    Human Evolution Speeding Up” (Podcast)
    Modern Life’s Pressures May Be Hastening Human Evolution” (Podcast)
    Who Was Adam? by Fazale Rana with Hugh Ross (Book)
    RTB Live! Vol. 15: Exploring the Origin of the Races with Fazale Rana (DVD)

  • Science News Flash: Has the Last Universal Common Ancestor Been Identified?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 28, 2016

    Researchers from Germany made headlines by announcing that they are one step closer to identifying LUCA (the last universal common ancestor)—the single-celled organism that anchors the evolutionary tree of life.1

    Because an organism’s genes reflect its environment, these researchers attempted to partially reconstruct LUCA’s genome. They reasoned that this reconstruction would tell them something about LUCA’s complexity and lifestyle.2 To accomplish this task, the researchers searched 6.1 million protein-coding genes found in archaeal and bacterial genomes for those with a special type of history (that is, they searched for universal, monophyletic genes).

    They identified 355 types of genes that fit their criteria. A few of the genes appear to be involved with essential biochemical operations such as DNA replication, transcription, and translation. On the other hand, most of the 355 genes play highly specialized roles that reflect a thermophilic lifestyle. For example, they discovered an enzyme called reverse gyrase that is only found among microbes that live in high-temperature environments. They also discovered enzymes that are part of a metabolic route called the Wood-Ljungdahl pathway. This pathway uses molecular hydrogen as an electron donor, and carbon dioxide as an electron acceptor. The hydrogen had to come from a geological source. On this basis, the German scientists concluded that LUCA lived in a hydrothermal vent environment, providing a ready source for this life-giving gas.

    The researchers also discovered that this microbe was able to: 1) fix nitrogen from the environment, incorporating this atom into it’s biomolecules; 2) lived in an anaerobic environment (devoid of oxygen); but 3) didn’t seem to have the ability to make amino acids. The investigators think that LUCA, though primitive, may have had more than 355 genes. If the investigators relax their search requirements a bit, they estimate that LUCA may have had nearly 575 genes.

    The German research team argued that not only was LUCA a thermophile, but that the origin of life occurred at hydrothermal vents.

    Have these researchers provided us with a key insight into LUCA’s identity? Have they identified the locale for the origin of life?

    Not necessarily. Here are some points to consider:

    In other words, there are good scientific reasons to question the high-temperature origin of life and the thermophilic identity of LUCA. And given the apparent complexity of LUCA, there is a strong basis to question evolutionary scenarios for life’s start.

    In spite of the headlines, scientists have no true understanding of how chemical evolution could have produced the first life on Earth.

    Resources
    Too Hot to Handle” by Fazale Rana (Article)
    Some Like It Hot—First Life Did Not” by Fazale Rana (Article)
    Sea Vents Closed as Life-Origin Site” by Fazale Rana (Article)
    Biochemists Ask, ‘How Low Can Life Go?’” by Fazale Rana (Article)
    Origins of Life by Fazale Rana and Hugh Ross (Book)
    Creating Life in the Lab by Fazale Rana (Book)

    Endnotes
    1. Madeline C. Weiss et al., “The Physiology and Habitat of the Last Universal Common Ancestor,” Nature Microbiology 1 (July 2016): 16116, doi:10.1038/NMICROBIOL.2016.116; James O. McInerney, “Evolution: A Four Billion Year Old Metabolism,” Nature Microbiology 1 (July 2016): 16139, doi:10.1038/NMICROBIOL.2016.139.
    2. Scientists think that LUCA was a prokaryotic, single-celled microbe.
  • Like a Fish Out of Water: Why I'm Skeptical of the Evolutionary Paradigm

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 27, 2016

    I am skeptical that evolutionary processes can fully account for life’s origin, history, and design—and that often makes me feel like a fish out of water.

    “Mainstream” scientists view biological evolution as the organizing principle in biology. In fact, Russian geneticist Theodosius Dobzhansky famously wrote, “Nothing in biology makes sense except in the light of evolution.”1 So, when I question evolutionary explanations, I become an outsider. I am outside the fish bowl, looking in. Because I’m a biochemist, my critics accuse me of being either dishonest or incompetent. Why else would I question the “fact” of evolution in the face of the overwhelming evidence for common descent? They claim that theological—not scientific motivations fuel my skepticism.

    I would partially agree with that assessment. I find it hard to square certain features of the evolutionary framework with some of Christianity’s most important biblical and theological ideas. But, I also think that there are some very real scientific problems associated with the evolutionary paradigm. The deficiencies are best exposed by failed predictions.

    From my perspective, the unpredicted pervasiveness of convergence justifies skepticism about evolution’s capacity to fully account for the history and diversity of life on Earth. Convergence stands as a failed prediction.

    Convergence

    One of evolution’s failed predictions relates to the phenomenon known as convergence. This concept describes instances in which unrelated organisms possess nearly identical anatomical and physiological characteristics. Presumably, evolutionary pathways independently produced these identical (or near identical) features. Yet convergence doesn’t make much sense from an evolutionary perspective. Indeed, if evolution is responsible for the diversity of life, one would expect convergence to be extremely rare. As a I wrote in a previous blog post, the mechanism that drives the evolutionary process consists of an extended sequence of unpredictable, chance events. Given this mechanism, it seems improbable that disparate evolutionary pathways would ever lead to the same biological feature. To put it another way, examples of convergence should be rare.

    The concept of historical contingency embodies the notion that evolution should be nonrepeatable, and is the theme of Stephen Jay Gould’s book Wonderful Life.2 To help clarify the concept of historical contingency, Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

    Yet, biological convergence is widespread.3 Recently, researchers from the University of New South Wales (in Australia) added to the examples of convergence at an organismal level. From an evolutionary perspective, they showed that amphibious behavior in fish evolved 33 separate times among extant groups! In fact, in one family, fish adopted a terrestrial life style between 3 to 7 times.

    This result was unexpected. One of the researchers involved with the study stated, “Because of the challenges fish face in being able to breathe and move and reproduce on land, it had been thought this was a rare occurrence.”4

    Recently, another team of investigators from the University of Kansas identified another example of biochemical convergence. They showed that venom evolved, separately and independently, 18 times in fish that live in freshwater and marine environments. This result is all the more surprising because—as William Leo Smith, one of the study’s authors points out— “fish venoms are often super complicated, big molecules.”5

    Does the Widespread Occurrence of Convergence Falsify Evolution?

    From my perspective, the unpredicted pervasiveness of convergence justifies skepticism about evolution’s capacity to fully account for the history and diversity of life on Earth. It stands as a failed prediction. Yet many evolutionary biologists don’t see it that way. For example, the scientists from the University of New South Wales responded to their unexpected find this way: “Now we have shown this initial transition to land is quite common, it seems these challenges can be readily overcome.”6 However, their interpretation entails circular reasoning. Biologists thought that fish moving to land would be difficult given the immense challenges associated with this transition. But, when it was found to be a frequent occurrence, then they conclude it must be easy. But they have no reason to think it must be easy other than the widespread occurrence of this transition. I would contend that this circular reasoning reflects a deep-seated, a priori commitment to the evolutionary paradigm, in which evolution is accepted as fact, and no evidence can ever count against it.

    Convergence and the Case for Intelligent Design

    Though the idea of convergence fits awkwardly within the evolutionary framework, it makes perfect sense if a Creator is responsible for life. Instead of convergent features emerging through repeated evolutionary outcomes, they could be understood as reflecting the work of a Divine mind. The repeated origins of biological features equate to the repeated creations by an intelligent Agent who employs a common set of solutions to address a common set of problems facing unrelated organisms.

    Resources
    The Cell’s Design (book)

    Endnotes
    1. Theodosius Dobzhansky, “Nothing in Biology Makes Sense Except in the Light of Evolution,” American Biology Teacher 35 (March 1971): 125–29.
    2. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W.W. Norton & Company, 1990).
    3. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
    4. University of New South Wales, “Fish Out of Water Are More Common Than Thought,” ScienceDaily, June 22, 2016, https://www.sciencedaily.com/releases/2016/06/160622102129.htm.
    5. University of Kansas, “Researchers Tally Huge Number of Venomous Fishes, Tout Potential for Medical Therapies,” ScienceDaily, July 5, 2016, https://www.sciencedaily.com/releases/2016/07/160705160206.htm.
    6. “Fish Out of Water,” ScienceDaily.
  • Historical Contingency and the Improbability of Protein Evolution, Part 2 (of 2)

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 20, 2016

    A few weeks ago, Kathy Emmons of WORD FM in Pittsburg interviewed me about the connection between human evolution and human trafficking. During the interview, she asked me if theological or scientific concerns drove my skepticism about human evolution. My answer is both.

    I find it difficult to reconcile the idea of human evolution with passages in the Old and New Testaments that address human origins. But, I also think that there are significant scientific problems confronting the evolutionary paradigm. A recent study by scientists from the Universities of Oregon and Chicago highlights one of those scientific challenges.1

    As described in a previous post, these researchers wanted to develop a better understanding of the role that chance historical events play in evolutionary processes. To do this, they reconstructed what they believe to be the evolutionary pathway that led to the emergence of the cortisol-specific glucocorticoid receptor protein, a key component of the vertebrate endocrine system. Based on their reconstruction, it appears that seven amino acid changes transformed the ancestral receptor protein into one that exclusively binds cortisol. They determined that two of the changes were permissive. That is, these changes do not contribute to the binding specificity of the glucocorticoid receptor, but must occur before any of the functional changes took place. Based on their analysis, it appears that the permissive changes were highly improbable, leading the researchers to conclude that historical contingency plays a central role in evolutionary transformations.

    According to the researchers:

    “If evolutionary history could be replayed from the ancestral starting point, the same kind of permissive substitutions would be unlikely to occur. The transition to GR’s [glucocorticoid receptor’s] present form and function would likely be inaccessible, and different outcomes would almost certainly ensue. Cortisol-specific signaling might evolve by a different mechanism in the GR . . . or the vertebrate endocrine system more generally—would be substantially different.”2

    Historical Contingency

    The concept of historical contingency is the theme of the late Stephen Jay Gould’s book Wonderful Life.3 According to this idea, the evolutionary process consists of an extended sequence of unpredictable, chance events. To help clarify this concept, Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

    Gould envisioned historical contingency as primarily resulting from external events (such as climate change or asteroid impacts). But this latest work indicates that the intrinsic complexity of proteins also contributes to historical contingency, because of the necessity and low probability of of permissive amino acid substitutions that support functional changes.

    How Widespread Is Historical Contingency?

    The question then becomes: How widely applicable is this result? The research team from the Universities of Oregon and Chicago expressed uncertainty regarding this point, but other studies indicate that historical contingency must play a prominent role in molecular evolution.

    For example, the long-term evolution experiment conducted by Richard Lenski’s group at Michigan State University demonstrated that the emergence of citrate metabolism in E. coli under aerobic conditions was historically contingent, predicated on a sequence of chance molecular events. (For more information, see the articles listed under “Resources.”)

    Using simulations to monitor the evolution of a protein dubbed argT, researchers from the University of Pennsylvania showed that genetic mutations selected by the evolutionary process are dependent on previous mutations, and over time it becomes increasingly difficult to reverse mutational transformations.4 In other words, an amino acid substitution that occurs in a protein today and is accepted by the evolutionary process would most likely be deleterious if it occurred in the past (because of the central role permissive substitutions play in evolutionary history). Consequently, this mutational change would be selected against by the evolutionary process. One of the researchers involved in this study, Joshua Plotkin, stated,

    “There is intrinsically a huge amount of contingency in evolution. Whatever mutations happen to come first set the stage for what other later mutations are permissible. Indeed, history channels evolution down a certain path. Gould’s famous tape of life would be very different if replayed, even more different than Gould might have imagined.”5

    A Failed Prediction of the Evolutionary Paradigm

    Because the evolutionary process is historically contingent, it seems unlikely that evolutionary processes would lead to identical or nearly identical outcomes. Yet, when viewed from an evolutionary standpoint, it appears as if repeated evolutionary outcomes have been a common occurrence throughout life’s history. This phenomenon—referred to as convergence—is widespread. Evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books Life’s Solution and Convergent Evolution, that identical evolutionary outcomes are a characteristic feature of the biological realm.6 Scientists see these repeated outcomes at the ecological, organismal, biochemical, and genetic levels. In fact, in my book The Cell’s Design, I describe 100 examples of convergence at the biochemical level.

    I regard the widespread occurrence of convergence to one of evolution’s failed predictions, and, as I told Kathy Emmons, a justifiable reason to be skeptical of the claim that evolutionary processes can fully explain the history, diversity, and design of life.

    In an upcoming blog post, I will further explore the challenge convergence poses for the evolutionary paradigm.

    Stay tuned… (or set your tape player to “record.”)

     

    Resources

    Endnotes
    1. Michael Harms and Joseph Thornton, “Historical Contingency and Its Biophysical Basis in Glucocorticoid Receptor Evolution,” Nature 512 (August 2014): 203–07, doi:10.1038/nature13410.
    2. Ibid., 207.
    3. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W.W. Norton & Company, 1990).
    4. Premal Shah, David McCandlish, and Joshua Plotkin, “Contingency and Entrenchment in Protein Evolution under Purifying Selection,” Proceedings of the National Academy of Sciences, USA 112 (June 2015): E3226–E3235, doi: 10.1073/pnas.1412933112.
    5. University of Pennsylvania, “Evolution Is Unpredictable and Irreversible, Biologists Show,” ScienceDaily, June 8, 2015, sciencedaily.com/releases/2015/06/150608213032.htm.
    6. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
  • Science News Flash: Stone Tool Use by Capuchin Monkeys Challenges Human Evolution

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 14, 2016

    I love cashew nuts! Apparently, so do capuchin monkeys.

    A team of scientists from Oxford University (in the UK) and the University of Sao Paulo (in Brazil) report that capuchin monkeys in the northeast forests of Brazil make sophisticated use of stone tools to extract cashew nuts from shells.1

    These researchers claim that this find sheds light on the evolution of human behavior. However, I take a different view. I maintain that this discovery actually undermines the standard model for human evolution. At the same time, this work highlights human exceptionalism, which finds ready explanation in the biblical human origins account.2

    Tools Engender New Scientific Possibilities

    This discovery, reported in the journal Current Biology, has found its way into popular science outlets, spurring headlines such as “Scientists Unearthed a Trove of 700-Year-Old Stone Tools—Used by Monkeys.” And with good reason. It is the first archaeological evidence for the use of stone tools by nonhuman primates outside of Africa, suggesting a whole new arena of scientific investigation. Lydia Luncz, a member of the research team, stated, “We think we’re just at the beginning.”3

    To get to cashew nuts, capuchins go through an elaborate process. These monkeys carefully select large flat sandstones and quartzite to use as an anvil and hammer, respectively. They transport these stones to the base of the cashew trees. There, they place the cashew nut on the flat anvil (which is about four times the size of the hammer) and carefully strike the shell with the hammer (which is about four times the size of an average stone) breaking it open so they can get to the nut inside. Once they are done with the tools, the capuchins leave them at the base of cashew trees. A walk through the forest reveals a number of cashew nut processing centers, established by these industrious creatures.

    To determine how long capuchins have engaged in this behavior, the research team excavated beneath several cashew trees located in the Brazilian forest. They discovered stone tools at least 2 feet beneath the surface that date back to about 700 years old. The excavated tools had a dark organic residue on them. Analysis of the residue indicates that it is the leftover remnants of cashew nuts, confirming the use of these stones as tools. Based on the excavations, it appears that about 100 generations of capuchins have employed stone tools to extract cashews from shells. It is reasonable to think that this behavior extends even further back in time.

    This discovery follows on the heels of earlier work by the same team. In a previous study, these scientists observed Burmese long-tailed macaques in Thailand using stone tools to crack open shellfish, crabs, and nuts. Excavations at macaque sites on the island of Piak Nam Yai have identified stone tools that are about 65 years in age, going back two generations.

    The use of stone tools among nonhuman primates is not limited to capuchins and macaques. Researchers have also uncovered evidence for chimpanzee stone tool use in Africa that dates back to over 4,000 years ago.

    It seems as if hominids aren’t the only primates to leave behind an archaeological record.

    Tools Throw Evolution into Question

    The use of stone tools by capuchins, macaques, and chimpanzees has important implications for the creation-evolution debate. The tools used by these nonhuman primates is reminiscent of tools used by hominids. The similar behavior of hominids, Great Apes, and Old and New World monkeys renders the activities of hominids much less remarkable. I wrote elsewhere about the implications of tool use by chimpanzees (see here). The point I raised applies to the use of stone tools by capuchins and macaques:

    “Chimpanzee behavior is closer to what we infer about hominid behavior from the fossil record, particularly Homo habilis and Homo erectus. These creatures, too, made tools and engaged in hunting and scavenging activity. The temptation is to see hominid behavior as transitional, representing a path to modern human behavior. Yet the newly recognized behavior of chimpanzees distances the hominids from modern humans. Just because the habilines and erectines made tools and engaged in other remarkable behaviors doesn’t mean that they were ‘becoming human.’ Instead, their behavior appears to be increasingly animal-like, particularly when compared to chimp activities.”4

    And, I would add, hominid behavior becomes even more animal-like when compared to the behavior of capuchins and macaques.

    Resources
    Who Was Adam? (book)
    Chimpanzee’s Behavior Supports RTB’s Model for Humanity’s Origin” (article)
    Chimpanzees’ Sleeping Habits Closer to Hominid Behavior Than to Humans’” (article)

    Endnotes
    1. Michael Haslam et al., “Pre-Columbian Monkey Tools,” Current Biology 26 (July 2016): pR521–R522, doi:10.1016/j.cub.2016.05.046.
    2. RTB’s biblical creation model for human origins views the hominids as creatures, created by God’s divine fiat, possessing intelligence and emotional capacity. These animals were able to employ crude tools and even adopt some level of “culture,” much like baboons, gorillas, and chimpanzees. But they were not spiritual beings made in God’s image. That position—and all of the intellectual, relational, and symbolic capabilities that come with it—remains reserved for modern humans alone.
    3. Darryl Fears, “Scientists Unearthed a Trove of 700-Year-Old Stone Tools—Used by Monkeys,” The Washington Post, July 11, 2016, https://www.washingtonpost.com/news/animalia/wp/2016/07/11/in-brazil-scientists-unearth-a-trove-of-ancient-stone-tools-used-by-monkeys/.
    4. Fazale Rana, “Chimpanzees’ Sleeping Habits Closer to Hominid Behavior Than to Humans,'” Today’s New Reason to Believe (blog), Reasons to Believe, June 9, 2014, https://www.reasons.org/articles/chimpanzees-sleeping-habits-closer-to-hominid-behavior-than-to-humans.
  • Historical Contingency and the Improbability of Protein Evolution, Part 1 (of 2)

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 13, 2016

    Can evolutionary processes produce biological innovation?

    Critics of the evolutionary paradigm—including me—would say, “No.” However, the reasons for my skepticism differ from many of evolution’s chief detractors. One argument against the evolutionary paradigm that causes me discomfort has to do with the “improbability” of the evolutionary process. For example, one common version of this argument relates to the evolutionary emergence of proteins, with critics asserting that the evolution of novel proteins from preexisting proteins would have been so improbable that it defies an evolutionary explanation. To justify this position, these critics often point to studies such as the one published by scientists from the Universities of Oregon and Chicago that seemingly buttresses their point.1 But does it?

    The Evolutionary Origin of a Protein Receptor

    This research team hoped to gain insight into the role that chance historical events play in evolutionary processes. Working within the framework of the evolutionary paradigm, they determined what they believe to be the amino acid sequence and structure of the ancestral protein that evolved into the cellular receptor protein that binds the hormone cortisol. They claim to have resurrected an ancient protein they believe existed 450 million years ago, before the cortisol-specific glucocorticoid receptor evolved its specificity for this particular hormone.2

    Today, the cortisol-specific glucocorticoid receptor assumes a key role in the endocrine system by regulating development and the stress response. The activity of this protein is mediated by cortisol binding. However, the researchers believe that in the past the ancestral protein was biochemically promiscuous, binding a number of hormones, and only later evolved its specificity for cortisol through amino acid changes mediated by the putative evolutionary process. Based on a reconstruction of the evolutionary pathway, they conclude that seven amino acid changes transformed the ancestral receptor protein into one that exclusively binds cortisol.

    The researchers classified the changes into two categories: 1) functional; and 2) permissive. They deemed five of the changes as functional, meaning that these changes contributed to the receptor’s cortisol-binding specificity. They dubbed the other two changes as permissive. These changes do not contribute to the binding specificity of the glucocorticoid receptor, but must occur for the functional changes to take effect. In other words, if the functional changes took place independently of the permissive changes, the resulting hormone receptor would not bind cortisol. The researchers determined that the permissive changes help to stabilize the receptor protein’s structure so that it can tolerate the five functional changes.

    Because cortisol binding depends upon the permissive mutations, the researchers reasoned that historical contingency must have played some role in the evolution of the cortisol-specific receptor protein. The permissive mutations must have appeared first, because if they didn’t, the functional changes would not have been selected (again) since they aren’t functional apart from the permissive changes.

    The Improbability of Protein Evolution

    The question then becomes, “How prominent is contingency in the evolutionary history of the cortisol-specific receptor protein?” To address this point, the investigators synthesized the ancestral receptor protein with the five functional amino acid changes (AP+5). Then, they subjected the AP+5 protein to random amino acid changes to try and determine the number of possible alternate permissive changes that could stabilize the receptor protein in the same way as the historical permissive changes.

    They screened about 12,500 random variants of the AP+5 protein. These variants yielded an estimated 1,025 unique single amino acid replacements, 1,802 unique double amino acid replacements, and 825 unique higher order combinations of amino acid substitutions. That is, they examined about 3,650 variants of the AP+5 protein. (The other 8,850 variants were duplicates of the 3,650 variants.) They also engineered 10 additional AP+5 variants using rational design principles. To their surprise, none of the 3,660 variants (3,650 in the screened library, plus the additional 10 engineered double mutants) yielded a functional cortisol-specific receptor that would not disrupt the function of the ancestral protein. (Four of the AP+5 variants displayed cortisol-specific binding, but these four changes destroyed the function of the ancestral protein. From an evolutionary perspective, these alternate permissive substitutions would have been selected against because of their disruptive influence.)

    This result indicates that it is highly improbable that the permissive amino acid changes necessary to support the evolution of a cortisol-specific receptor protein could ever occur (with an upper bound of 0.03 percent). The researchers conclude:

    “The total frequency is probably far lower…The universe of possible variants containing two or more replacements is very large, so alternative permissive sets may exist; however, these genotypes would require multiple independent substitutions, and the joint probability of such events would be very low because they cannot be acquired deterministically by selection for the derived function.”3

    Their probability assessment doesn’t even include the likelihood of the five functional changes occurring after the two permissive changes took place, meaning that the probabilities for the evolution of the cortisol-specific receptor protein from a promiscuous ancestral receptor are even more unlikely.

    The Contingency of the Evolutionary Process

    As a skeptic of the evolutionary paradigm, it is tempting to point to this study as evidence that evolutionary transformations are so improbable that these processes cannot account for biological innovation. But this would be an unfair conclusion that misrepresents the way evolutionary biologists interpret these results. Instead, these scientists argue that these results tell them something about the evolutionary process: Namely, that historical contingency plays a central role in evolutionary transformations.

    The concept of historical contingency is the theme of the late Stephen Jay Gould’s book Wonderful Life.4 According to this idea, the mechanism that drives the evolutionary process consists of an extended sequence of unpredictable, chance events. To help clarify this concept, Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

    According to the researchers:

    “If evolutionary history could be replayed from the ancestral starting point, the same kind of permissive substitutions would be unlikely to occur. The transition to GR’s [glucocorticoid receptor’s] present form and function would likely be inaccessible, and different outcomes would almost certainly ensue. Cortisol-specific signaling might evolve by a different mechanism in the GR—or the vertebrate endocrine system more generally—would be substantially different.”5

    A Flawed Argument

    In other words, while evolutionary transformations are highly improbable, their unlikelihood cannot be used as a legitimate basis for skepticism about the evolutionary paradigm. To use them in this way would be to make a straw man argument against biological evolution. This probability argument assumes that evolutionary end points are fixed, but evolutionary biologists don’t see them that way at all—because of the historically contingent nature of the process.

    Still, there are some legitimate reasons to be skeptical about the capacity of evolutionary mechanisms to account for the design and diversity of life. And one of those reasons is exposed by this study and the historically contingent nature of the evolutionary process.

    I will elaborate in my next blog post.

    Resources

    Endnotes
    1. Michael Harms and Joseph Thornton, “Historical Contingency and Its Biophysical Basis in Glucocorticoid Receptor Evolution,” Nature 512 (August 2014): 203–7.
    2. For a Christian perspective on resurrected ancient proteins, see my article, Fazale Rana, “Resurrected Proteins and the Case for Biological Evolution,” Today’s New Reason to Believe (blog), Reasons to Believe, October 14, 2013, https://www.reasons.org/articles/resurrected-proteins-and-the-case-for-biological-evolution.
    3. Harms and Thornton, “Historical Contingency,” 204.
    4. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton & Company, 1990).
    5. Harms and Thornton, “Historical Contingency,” 207.
  • Science News Flash: Reinterpretation of Sea Worm Fossil Challenges Evolution

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 08, 2016

    In a recent article published by the BBC, researchers from the University of Toronto announced the reinterpretation of an enigmatic fossil, Oesia disjuncta, now classifying this creature as a hemichordate.1 They also now think that tube-like structures, originally thought to be a type of seaweed, were made by Oesia.

    This reinterpretation was based on the recovery of new fossil specimens from Marble Canyon in the Canadian Rockies. Oesia disjuncta is part of a fossil assemblage known as the Cambrian explosion, so researchers estimate the creature’s age to be around 510 million years old. (The Cambrian explosion refers to a dramatic event in life’s history in which 50 to 80 percent of all known animal phyla appear in a geological instant.)

    According to lead researcher in the study, Karma Nanglu:

    Hemichordates are central to our understanding of how deuterostomes evolved.2

    I would partially agree with Nanglu: Hemichordate fossils are central to our understanding of life’s history; but instead of shedding light on evolutionary history, I would maintain that the appearance of this phylum during the Cambrian explosion creates problems for the evolutionary paradigm. (To learn why I hold this view see my article “Cambrian Flash.”) At the same time, this find adds to the evidence for the scientific credibility of the Genesis 1 creation account. (For details see my article “The ‘Great Unconformity’ and the Cambrian Explosion Conform to the Genesis 1 Creation Account.”)

    For more on the Cambrian explosion, check out the following resources.

    Endnotes
    1. Karma Nanglu et al., “Cambrian Suspension-Feeding Tubicolous Hemichordates,” BMC Biology 14 (July 2016): 56, doi: 10.1186/s12915-016-0271-4.
    2. “Sea Worm Fossil Gives Clues to ‘Common Ancestor,’” Science & Environment (blog), BBC News, July 7, 2016, https://www.bbc.com/news/science-environment-36724562.
  • Adam and Eve: A Primordial Pair or a Population?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 06, 2016

    Today, one of the central science-faith issues facing evangelical Christianity centers around the historicity of Adam and Eve. Did Adam and Eve actually exist? Or are they merely mythical, functioning as theological constructs meant to represent every man and every woman? And if they did exist, were they the primordial pair that gave rise to all humanity? Or were they representatives, part of a population?

    My ministry activities during the month of June reminded me of the importance of these questions. I participated in the Dabar Conference, which centered on “Reading Genesis in an Age of Science,” so naturally, there was much discussion about the identity of Adam and Eve. I also taught a weeklong intensive course for Southern Evangelical Seminary on the biblical and scientific perspectives on human origins. As part of the course, we explored the scientific case for Adam and Eve’s historicity and the importance of this idea for the Christian faith. And finally, at the end of the month, I taught at the RZIM Summer Institute, where we examined the relationship between the biblical account of human origins and the key tenets of Christian ethics.

    Adam and Eve’s existence and relationship to humanity are not merely academic concerns. Instead, these questions influence key doctrines of the Christian faith such as: inerrancy, the image of God, the Fall, original sin, marriage, and the atonement. Because of the importance of a historical Adam and Eve to the Christian faith, it is important to be able to demonstrate the scientific credibility of the biblical view of human origins.

    A Scientific Case for a Historical Adam and Eve

    Part of the scientific support for the traditional biblical view comes from work in molecular anthropology. One of the most important advances in human origins research has been the use of DNA sequence data to gain insight into the origin and early history of humanity.

    Of particular interest are the results of mitochondrial DNA and Y-chromosomal studies that trace humanity’s origin to single ancestral sequences referred to as “mitochondrial Eve” and “Y-chromosomal Adam.” These ancestral sequences correspond to single female and male individuals. I interpret mitochondrial Eve and Y-chromosomal Adam as pointers to the biblical Adam and Eve.

    Many evolutionary biologists reject the notion that mitochondrial Eve and Y-chromosomal Adam were the original biblical couple. Instead, they argue that human beings originated as a population. Accordingly, there were many “Eves” and “Adams.” In other words, we descend from the two who were lucky enough for their genetic material to persist to the present. The genetic lines of the other first humans were lost over time.

    Perhaps most challenging to the view that mitochondrial Eve and Y-chromosomal Adam are the biblical Adam and Eve are the population size estimates determined from human genetic diversity data. These methods all indicate that the initial human population size was never less than several thousand individuals. It is largely based on these results that evolutionary biologists argue that mitochondrial Eve and Y-chromosomal Adam weren’t the primordial pair.

    5 Reasons Why Humanity Didn’t Begin as a Population

    Evolutionary biologists argue for this mainstream idea (that there were many first humans, not just two), but I’m reluctant to accept these claims for a number of reasons.1

    1. The idea that humanity arose as a population is a theory-laden concept that is a necessary entailment of the evolutionary paradigm. Biologists view evolution as a population-level phenomenon. Populations evolve, individuals don’t. As a consequence, there can’t be a primordial pair—if one views human origins from an evolutionary framework. To put it another way, humans must have emerged from a population by definition.
    2. The methods used to determine population sizes rely on simplified and idealized mathematical models that are highly sensitive to input parameters. Because of that the population numbers need to be viewed as rough estimates, at best.
    3. These models do a poor job in taking into account the effects of population structure, migrations, and gene flow all of which can lead to misleading population size calculations.2
    4. Population size methods have not been validated. That is, there are not any studies that demonstrate that these methods produce accurate results for population size estimates, when applied to known situations. Studies in conservation biology suggest that these models don’t accurately predict genetic variability when the original population size is known. As a case in point, in three separate studies involving Mouflon sheep, Przewalski’s horses, and gray whales, genetic diversity (measured generations after the initial population) was much greater than expected based on the models.
    5. Other studies in conservation biology raise questions about the validity of the mathematical relationships that undergird the population size methods. In fact, these concerns prompted one research team to question if these problems invalidate population size estimates in humans. These researchers state, “Recently, however, Bazin et al. (2006) have argued that mtDNA variation is a poor indicator of population size in animals. . . . This raises the question of whether mtDNA is in fact a reliable predictor of human population size.”3

    Did Humanity Begin as a Pair?

    Because of the central importance of Adam and Eve’s historicity to the Christian faith, I am reluctant to embrace the idea that humanity began as a population, not a pair. But, I’m as equally reluctant to accept this scientific claim—mainstream or not—knowing that the population size measurements are based on simplified, idealized methods that struggle to take into account population dynamics that can influence population size estimates and haven’t been validated. Questions about the validity of the mathematical relationships that form the basis of these methods compound these problems. To put it another way: Even if I accepted the notion of common descent, I still wouldn’t be convinced that humans arose as a population because of the scientific questions that surround the population size estimates.

    In my view, science has yet to falsify the notion that humanity descended from a primordial pair.

    Resources

    Endnotes
    1. Some of my concerns with population size estimates are also detailed in the article, Fazale Rana, “Were They Real? The Scientific Case for Adam and Eve,” Today’s New Reason to Believe (blog), Reasons to Believe, October 1, 2010, https://www.reasons.org/articles/were-they-real-the-scientific-case-for-adam-and-eve.
    2. For example, see Olivier Mazet et al., “On the Importance of Being Structured: Instantaneous Coalescence Rates and Human Evolution—Lessons for Ancestral Population Size Inference?” Heredity 116 (April 2016): 362–71, doi:10.1038/hdy.2015.104; Thomas Broquet et al., “Genetic Bottlenecks Driven by Population Disconnection,” Conservation Biology 24 (December 2010): 1596–1605, doi:10.1111/j.1523-1739.2010.01556.x.
    3. Quentin Atkinson, Russell Gray, and Alexei Drummond, “mtDNA Variation Predicts Population Size in Humans and Reveals a Major Southern Asian Chapter in Human Prehistory,” Molecular Biology and Evolution 25 (February 2008): 468–74, doi:10.1093/molbev/msm277.

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