Biochemical Finite-State Machines Point to an Infinite Creator

by Fazale RanaSeptember 22, 2021

During my time as a graduate student studying biochemistry at Ohio University, I spent many long days—and nights—working in the laboratories housed in the Clippinger Building, home to the chemistry and physics departments.

Sometimes the only food I had available to me—particularly during those late nights that turned into the early hours of the morning—were the vending machine snacks in the common area of the second floor.

Unfortunately, the vending machine didn’t always work. It wasn’t unusual to walk into the common area to find someone pounding on the machine in frustration.

A vending machine is a physical instantiation of an abstract machine called a finite-state machine. (More on finite-state machines [FSMs] below.) Recently, a team of biophysicists at the University of California, San Francisco (UCSF) discovered that unicellular organisms belonging to the group Euplotes employ a biochemical FSM. This machine regulates the “walking” behavior of these single-celled creatures as they make their way across solid surfaces using leg-like appendages called cirri.1

This insight has far-reaching scientific implications, pointing to a general model that may explain the sophisticated behavior displayed by many different types of single-celled organisms. The work also carries significant philosophical—even theological—implications. It contributes to the revitalized Watchmaker argument for God’s existence and necessary role in the origin and design of life, as I first presented in my book The Cell’s Design.

To fully appreciate the philosophical significance of this discovery, a bit of background information on FSMs is in order.

Finite-State Machines
FSMs are considered to be abstract machines that mathematicians have devised to function as mathematical tools to model computational processes. Many real-world examples of FSMs can readily be found around us. In addition to vending machines (that take our money in return for a desired snack), other examples include turnstiles, elevators, traffic lights, and combination locks.

FSMs are defined by a set of states and inputs that trigger transitions from one state to another state (that may or may not be predetermined). An FSM can exist in any one of its defined states. And it can change or transition to another state based on a sequence of events or inputs presented to the FSM.

Of course, if the incorrect amount of money is inserted into the vending machine, it won’t change states because the input doesn’t match the predetermined value for input 1 or input 2. 

In its initial state (I), the vending machine is stocked with snacks that have been placed in a rack, waiting to be dispensed. When a hungry customer puts the correct amount of money in the machine (input 1) and then selects their snack of choice (input 2)—usually by pushing a predetermined sequence of numbers and letters on the control panel—the vending machine changes states (from I to A), delivering the desired food item. If the customer types in a different sequence of numbers and letters (input 3), the vending machine will transition to a different state (from I to B), delivering the alternative food item.

An FSM can be thought of as a type of mechanical computer that has limited memory and is restricted by the number of states that define it. In some vending machines, the same sequence of events (inputs) can trigger a different set of actions depending on the specific state of the FSM. For example, if the desired snack item is no longer available in the vending machine, punching the prescribed sequence of numbers and letters will no longer trigger the transition from one state to the other—at least, in some vending machines—because in this initial state (I’), the vending machine is no longer stocked with the desired snack item and can’t transition from I’ to A.

A Biochemical FSM
I learned some valuable lessons during my graduate and post-doctoral studies. One is this: sometimes when things go wrong during an experiment, they can lead to a significant scientific breakthrough—if you are willing to pay attention.

Such was the case for Ben Larson, a molecular life scientist at UCSF. Larson became frustrated by single-celled predators that contaminated and invaded his experiments, eating the cells he was trying to study.Eventually, he discovered that the invaders belonged to the genus Euplotes. These single-celled organisms live in fresh and saltwater environments. They move around by swimming, but they can also walk on surfaces using appendages on their underside.

Figure 1: Euplotes
Credit: Shutterstock

Larson and two collaborators became interested in how Euplotes “walked” on surfaces. Their walking behavior is sophisticated and complex, reminiscent of the gait displayed by complex multicellular organisms with brains and nervous systems. In fact, the behavior of some single-celled organisms is so complex and sophisticated—seemingly directed by some type of internal control—that some biologists have gone so far as to speculate that single-celled organisms possess a type of rudimentary nervous system. But they don’t.

So, how does Euplotes coordinate the movement of its cirri as it walks along surfaces?

By carrying out a frame-by-frame analysis of videos of Euplotes walking along a glass surface (in which Larson and his collaborators mapped out the position of each cirrus and mathematically modeled the organism‘s movements) the investigators concluded that some type of internal control was, indeed, directing and coordinating the cirri movements.

They speculated that the internal control was exerted by a network of microtubules just beneath the cell surface. Cirri are composed of microtubules, which are small, hollow tubules made of multiple copies of the protein tubulin. The tubulin subunits combine to form a molecular-scale tube. The arrangement of microtubules that form each cirrus extends into the internal space of the cell. These microtubules interlink with each other to form a microtubule network.


Figure 2: Microtubules
Credit: Shutterstock

When Larson and his collaborators disrupted the microtubule network, the coordinated movement of the cirri stopped. This finding implicates the microtubule network as the internal control regulating the behavior of the cirri. Based on the mathematical properties of the Euplotes gait, Larson and his research partners conclude that the microtubule network is a molecular-scale FSM—a mechanical nanocomputer. The microtubule network regulates the transition between a discrete set of gait states, with structural changes in the microtubule network corresponding to the different states of the system. Another way to think about the microtubule network is that it reflects an embodied set of computations that controls and coordinates the complex behavior of the cirri. Wallace Marshall, one of Larson’s collaborators, argues: “Our data shows you need microtubules for the computation to happen. The simplest explanation is that those are the computing elements.”3

The researchers think that this insight may have broad explanatory power. It may account for other sophisticated behaviors executed by single-celled organisms. That is to say, Larson and his collaborators think that an ensemble of FSMs may regulate several subcellular and cellular processes in which “decision-making” is required. Marshall concludes: “If you can make a computer out of microtubules, you can make a case for looking for them in many other cell types.”4

As remarkable as this insight may be from a scientific perspective, it is even more provocative when mulling over the philosophical and theological implications. To appreciate this point, we need to consider the classical Watchmaker argument advanced by William Paley.

The Watchmaker Argument
Eighteenth-century Anglican natural theologian William Paley (1743–1805) posited the Watchmaker argument in his 1802 work, Natural Theology or, Evidences of the Existence and Attributes of the Deity, Collected from the Appearances of Nature.

For Paley, the characteristics of a watch and the complex interaction of its precision parts for the purpose of telling time implied the work of an intelligent Designer. Paley asserted, by analogy, that just as a watch requires a watchmaker, so too, life requires a Creator, since biological systems display a wide range of features characterized by the precise interplay of complex parts for specific purposes.

Biomolecular Machines and the Revitalized Watchmaker Argument
In the last couple of decades, biochemists have discovered many proteins complexes inside the cell that are strict analogs to human-made machines with respect to their architecture, operation, and assembly. (For examples, see the articles listed in the Resources section.) The biomachines found in the cell’s interior reveal a diversity of form and function that mirrors the diversity of designs produced by human engineers. In many instances, this molecular-level biomachinery stands as a strict analog to human-made machinery. The one-to-one relationship between the parts of human-made machines and the molecular components of bio-machines is startling.

The discovery of biomolecular machines inside the cell imparts new vitality to the Watchmaker argument. The protein complexes inside the cell aren’t metaphorical machines—they are, in reality, actual machines. And Paley’s case continues to gain strength as biochemists continually discover new examples of biomolecular machines, such as the biochemical FSM made up of networks of microtubules.

Biochemical FSM and the Watchmaker Argument
The strict analogy between FSMs (which are both abstract entities and concrete real-world mechanical computers) and the regulatory behavior of microtubule networks in Euplotes is astoundingand provocative.

It goes without saying that when we encounter an FSM such as a vending machine, we recognize the design features of these devices. We also recognize that the decision-making capabilities of these systems were devised by intelligent agents. So, why shouldn’t we reach the same conclusion when we discover a biomolecular FSM inside the cell?

Resources

The Cell’s Design: How Chemistry Reveals the Creator’s Artistry by Fazale Rana (book)

Does New Approach Solve Origin-of-Life Problem?” by Fazale Rana (article)

Biomolecular Machines and the Watchmaker Argument

New Discovery Pumps Up Evidence for Design” by Fazale Rana (article)

A Biochemical Watch Found in a Cellular Heath” by Fazale Rana (article)

The Provocative Case for Intelligent Design: New Discovery Highlights Machine-Like Character of the Bacterial Flagellum” by Fazale Rana (article)

Manufacturing the Case for Intelligent Design” by Fazale Rana (article)

Electron Transport Chain Protein Complexes Rev Up the Case for a Creator” by Fazale Rana (article)

Biochemical Turing Machines ‘Reboot‘ the Watchmaker Argument” by Fazale Rana (article)

Responding to Challenges to the Watchmaker Argument

But Do Watches Replicate? Addressing a Logical Challenge to the Watchmaker Argument” by Fazale Rana (article)

Self-Assembly of Protein Machines: Evidence for Evolution or Creation?” by Fazale Rana (article)

Addressing the Concerns of a Critic and the Case for Intelligent Design” by Fazale Rana (article)

Nanodevices Make Megascopic Statement” by Fazale Rana (article)

A Cornucopia of Evidence for Intelligent Design: DNA Packaging of the t4 Virus” by Fazale Rana (article)

Endnotes

1. Ben T. Larson et al., “A Unicellular Walker Controlled by a Microtubule-Based Finite State Machine,” bioRxiv, preprint (June 17, 2021): doi:10.1101/2021.02.26.433123.
2. Michael Le Page, “Single-Celled Organism Has Evolved a Natural Mechanical Computer,” New Scientist, July 28, 2021.
3. Le Page, “Single-Celled Organism.”
4. Le Page, “Single-Celled Organism.“

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How Did Daniel Cope with Trauma during Captivity?

BY MARK CLARK – MAY 8, 2020

by Mark Clark

Humans in all eras of history have suffered trauma, especially from the horrors of war. How might people in the ancient world have coped with traumatic events without access to modern treatment options? Was coping even a possibility? We can learn much about trauma by looking to Daniel, a biblical figure who endured multiple severely traumatic events during his lifetime.

The Trauma of Captivity

Three common trauma triggers—wars, violence, and kidnapping—characterized the Babylonian captivity of the kingdom of Judah between roughly 605­ and 539 BC. Judah alone remained of the original nation of Israel after Assyria completely defeated the northern kingdom in 722 BC. The period of captivity began in this eastern Mediterranean region when Nebuchadnezzar defeated Egypt’s Pharaoh Necho at Carchemish in September 605 BC, taking modest plunder and some people from the region. Babylonian armies returned on three subsequent occasions to quell rebellions and take more Jews to Babylon, in 597, 586, and 582 BC.

The prophet Daniel and his three friends Hananiah, Azariah, and Mishael (more commonly known by their Babylonian names, Shadrach, Meshach, and Abednego) were taken in the first wave. Tens of thousands of Jews were taken in the subsequent waves of forced migration. A psalmist depicts the bitterness of the captivity in Psalm 137, where he laments the victimhood of the Jews in Babylon and ends in verses 8 and 9 with one of the harsher imprecations (curses) to be found in the whole book: “O Daughter of Babylon, doomed to destruction, happy is he who repays you for what you have done to us—he who seizes your infants and dashes them against the rocks.”

Here the psalmist demonstrates the two dominant characteristics of a traumatized person: seeing himself as a victim and wishing for vengeance. Marginal notes in the New International Version (NIV) of the Bible describe this psalmist as having returned to Jerusalem but still living with an unbearable past that continued to overwhelm his present.

Leading trauma researcher Bessel van der Kolk seems to affirm the plight of the captives by observing:

I am continually impressed by how difficult it is for people who have gone through the unspeakable to convey the essence of their experience. It is so much easier for them to talk about what has been done to them—to tell a story of victimization and revenge—than to notice, feel, and put into words the reality of their internal experience.[1]

How Daniel Coped

Unlike the psalmist, however, Daniel never exhibits victimhood or seeks vengeance. Instead, he consistently displays humility toward political authority and avoids seeking revenge against those of the court who conspired against him under King Darius. His near contemporary Ezekiel highly regarded Daniel’s wisdom and righteousness (Ezekiel 14:14­­–20Ezekiel 28:3). Remarkably, Daniel likely experienced much worse trauma than the Psalmist.

Daniel and his three friends were ripped from their families and homeland at an early age, probably 15. The military convoy that took them and other captives to Babylon would have taken 3­­­–4 months for a journey of some 900 miles over trade routes. In Babylon, they were stripped of their ethnic identity by being given names after the Babylonian gods. Worse still, they were likely emasculated (cf. Isaiah 39:5–­7 with Daniel 1:1–3a).

Any one of these events would be traumatic, but the combination of all of them would be overwhelming, unbearable, and incomprehensible. Such nightmarish trauma can result in the extreme condition called post-traumatic stress disorder, PTSD.

I believe Daniel found his way through the trauma of captivity by several means. Or, rather, God likely provided a “way of escape” to get him through this ordeal (1 Corinthians 10:13).

Van der Kolk articulates three modern therapies for trauma victims. They include

  1. talking, (re-) connecting with others, and allowing themselves to know and understand what is going on inside them, while processing the memories of the trauma (top-down approach);
  2. taking medicines that shut down inappropriate alarm reactions, or utilizing other technologies that change the way the brain organizes information; and
  3. allowing the body to have experiences that deeply and viscerally contradict the helplessness, rage, or collapse that result from trauma (bottom-up approach).[2]

The second, medicinal approach was not available to Daniel, but the first and the third would have been.

For evidence of the first approach, we see that Daniel maintains a small community of close friends who shared his experience and likely talked and encouraged one another. In Daniel chapter 2, we see them praying for each other and for Daniel to be able to interpret the king’s dream.

We also see evidence of the third approach. By walking most of the way to Babylon over the course of several months, Daniel would have engaged in the bilateral stimulation that therapists employ for a recent treatment of trauma called EMDR, eye movement desensitization and reprocessing. In a typical EMDR session, a therapist asks a client to hold different aspects of a traumatic event in mind and to visually track the therapist’s hand from side to side. Researchers believe this therapy is connected to biological mechanisms in REM sleep that victims use to begin processing their trauma and eventually become empowered. Psychologist Francine Shapiro developed the technique during a walk, and it has since been widely researched and validated.[3] Therapists use EMDR to help military veterans and other traumatized people recover from PTSD by enabling them to reprocess their experiences and to move on.[4]

Trauma victims need to do more than simply talk and walk, though. They also need to take “agency” over their lives. Van der Kolk notes: “‘Agency’ is the technical term for the feeling of being in charge of your life: knowing where you stand, knowing that you have a say in what happens to you, knowing that you have some ability to shape your circumstances.”[5]

I believe Daniel took “agency” over his life by committing to God’s kingdom purposes as found in Isaiah 49:6, submitting to God for his destiny:

It is too small a thing for you to be my servant to restore the tribes of Jacob and bring back those of Israel I have kept. I will also make you a light for the Gentiles, that you may bring my salvation to the ends of the earth.

Daniel exemplifies Isaiah 49:6 in two ways throughout his captivity. One, he was a light for the Gentiles. In both Babylon and Persia, every court official he encountered acknowledged that Daniel served the God of heaven. Two, he helped restore Israel. In Daniel chapter 9, he initiated the prayer of repentance that would release the Jewish captives back to their homeland, restoring the Messianic line in Judah.

Insight for Today

Daniel served God’s kingdom purposes for his day. Serving God in this way likely diminished the overwhelming trauma he surely experienced. And though his ordeal is a part of biblical revelation and not normative for us today, Daniel’s experience also shows that the remedies for trauma therapy evidenced in the Bible appear to be consistent with those of modern science. In this way the two sources of revelation are in harmony, as Christianity asserts.

Christians today can look to Daniel as a model of how we, too, may serve God’s kingdom purposes. Today, that means following Jesus in the Great Commission (Matthew 28:19) according to the pattern laid down by the apostle Peter:

But in your hearts set apart Christ as Lord. Always be prepared to give an answer to everyone who asks you to give the reason for the hope that you have. But do this with gentleness and respect, keeping a clear conscience.

1 Peter 3:15–16

 

Endnotes
  1. Bessel A. van der Kolk, MD, The Body Keeps the Score: Brain, Mind, and Body in the Healing of Trauma (New York: Viking, 2014), 47.
  2. Van der Kolk, 3.
  3. See EMDR Institute, Inc., founded by Francine Shapiro, PhD, http://www.emdr.com/francine-shapiro-ph-d/, accessed April 22, 2019.
  4. Francine Shapiro, PhD, and Margot Silk Forrest, EMDR: The Breakthrough “Eye Movement” Therapy for Overcoming Anxiety, Stress, and Trauma (New York: Basic Books, 2004).
  5. Van der Kolk, 95.

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Christianity and Human Rights: When Giving Up Our Rights Shows Love to Others

by Guest WriterStephen McAndrewSeptember 9, 2021

From protests in Myanmar because of the refusal to recognize the results of a democratic vote, to marches against racial discrimination in the United States, to movements to eradicate human trafficking, people all over the world recognize the importance of upholding human rights.  

Human rights are grounded in the fact that every human has inherent dignity. When we deny people their rights or extend those inherent rights to only some, we fail to respect that dignity. For example, Martin Luther King Jr. pointed out that racial discrimination degrades human personality by not treating people with dignity due to the color of their skin. He shared in “Letter From a Birmingham Jail” that his daughter cried when he had to tell her that she could not go to an amusement park because of racial discrimination.1

Philosopher Joel Feinberg imagined a world in which people are virtuous and adhere to moral duties, but in which there is no ability to claim when one’s rights have been violated. Feinberg argued this world would be morally flawed as it failed to recognize human dignity.The ability to claim that one’s rights have been violated recognizes human dignity. When we point out that the rights of other people have been abused, and work to vindicate and protect their rights, we treat that person with dignity. We treat them as if they matter—which they do.

The global community has recognized the importance of human rights and their grounding in human dignity. The Universal Declaration of Human Rights, adopted in the wake of World War II and its horrors, states that “recognition of the inherent dignity and of the equal and inalienable rights of all members of the human family is the foundation of freedom, justice and peace in the world.”3

However, some thinkers, like philosopher Charles Taylor, point out that relying on one’s rights can be problematic because it is based on individualism.4 For example, we have a right to control our property. If I have an assigned parking spot where I live, I can be indignant if someone parks in my spot. They violated my right to park there, I pay for the right to park there. How dare they! However, say an elderly neighbor is on their deathbed with people coming to visit them before they pass. There’s a limited number of parking spaces. If I insist no one can park in my spot, I am within my rights to do so. But it would be selfish of me not to surrender my right in this situation.

It’s often argued that we have a strict moral duty not to infringe on others’ rights (negative duties) but we are not morally obligated to help people in need if we have not violated their rights.This means that positive duties to help people are—as German philosopher Immanuel Kant called them—imperfect duties.5 This essentially means that we use discretion when choosing to help people and are not obligated to help everyone. Many people may see someone in need of help and not come to their aid, comforting themselves with the fact that since they didn’t cause this person’s suffering, they do no wrong by not helping them.

This means I have a moral duty not to park in someone else’s parking spot. However, I’ve no moral duty to give up my parking spot to someone else and, therefore, I’m not violating their rights by not giving them my spot. 

So, on the one hand, human rights recognize and, when enforced, protect the dignity of all people everywhere. However, on the other hand, focusing on my rights alone can cause me to be self-absorbed and selfish. How can these two things be reconciled? It is vital to recognize the importance of individuals. Yet a community of people focused solely on their own rights does not lead to a flourishing society. Is the solution to abandon the concept of human rights because it is based on individualism and can be used to justify selfishness? No, there is a model of treating individuals with dignity and, in doing so, protecting their rights while avoiding selfishness in the process.

Christianity, like Judaism, explains that all humans have dignity because we are created in the image of God (Genesis 1:26–27). Therefore, to respect the dignity of all people, we should protect human rights. But Christianity also supports giving up one’s rights in order to love others. For example, the Good Samaritan risked his physical safety and used his personal property to help the injured traveler. If the Good Samaritan held to the theory that he just had negative moral duties he could have walked by and not been compelled to help because he was not the one who attacked and robbed this poor man (Luke 10:25–37). Jesus pointed to this as the way we should love our neighbors—not claiming we have a right to absolute physical safety and an absolute right to use our personal property as we wish.

Moreover, Jesus is God and gave up his right to be treated as equal with God in order to show the depth of God’s love for humanity. Paul writes that Jesus:

Who, being in very nature God, did not consider equality with God something to be used to his own advantage; rather, he made himself nothing by taking the very nature of a servant, being made in human likeness. And being found in appearance as a man, he humbled himself by becoming obedient to death—even death on a cross! (Philippians 2:6–8)

There is no question that Jesus’s rights were grossly violated in the crucifixion. But he considered the worth of his sacrifice to be greater than the violation of those rights because his sacrifice meant the salvation of all humans who believe and follow him. This shows how Jesus valued the dignity of people.

The protection of human rights recognizes the immense value of people and leads to human flourishing, but we also need to recognize that our rights are not an excuse to focus solely on ourselves. Sometimes we need to give up our rights in order to love other people. Christianity provides us a perfect model in Jesus who surrendered himself as an act of love for us. We don’t have to abandon human rights as a way to avoid risking being self-absorbed. To do so would be a great loss.

Endnotes

  1. Martin Luther King Jr., “Letter From a Birmingham Jail,” African Studies Center, University of Pennyslvania (April 16, 1963).
  2. United Nations, “Universal Declaration of Human Rights,” un.org/en/about-us/universal-declaration-of-human-rights.
  3. Joel Feinberg and Jan Narveson, “The Nature and Value of Rights,” Journal of Value Inquiry 4 (December 1970): 243­–260, doi:10.1007/BF00137935.
  4. Charles Taylor, “A World Consensus on Human Rights,” Dissent, Summer 1996, dissentmagazine.org/article/a-world-consensus-on-human-rights.
  5. Immanuel Kant, Grounding for the Metaphysics of Morals, 3rd ed., trans. James W. Ellington (Indianapolis: Hackett Publishing, 1993).

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3 Things You May Not Know about Thomas Aquinas

by Kenneth SamplesSeptember 14, 2021

As a student of Christian history, I find the details of the lives of Christendom’s giants to be fascinating, inspiring, and even amusing. I hope that the following experiences in Thomas Aquinas’s life will do the same for you as you see the common humanity in our union with Christians from all times.

Many people consider St. Thomas Aquinas (1225–1274) to be the greatest thinker in the history of Christendom. A medieval scholastic philosopher and theologian, Aquinas’s system of thought (called “Thomism”) was declared the official philosophy of the Roman Catholic Church. In a life span of fewer than 50 years, he became a voluminous writer and masterful defender of classical Christian theism. Written almost 750 years ago, Summa Theologiae is arguably Aquinas’s magnum opus.

Yet, while he is one of the most famous philosophers in all of Western civilization, there are three things you may not know about Aquinas.1 You may find them surprising.

1. Thomas was ridiculed as a young person.

Thomas was born in the family castle of Roccasecca midway between Rome and Naples, Italy—the youngest son of the knight Landulf of Aquino (thus the name “Aquinas”) in the High Middle Ages. At the tender age of five, he began his schooling at the famous Abbey of Monte Cassino where he was educated by the priests and monks of the Benedictine order of the Catholic Church. He was heavyset and slow of speech as a young person so some of his fellow students called him “the dumb ox.” Ironically, Thomas was anything but unintelligent. He would go on to prove himself a philosophical and theological genius. In fact, Thomas may have possessed the brightest mind in Christian history.

2. Thomas’s parents opposed his desire to become a Dominican priest.

The Dominican Order, also known as the Order of the Preachers (OP), was founded by St. Dominic de Guzman in 1219. At nineteen, Thomas decided to join the order, but it didn’t carry the prestige and influence as that of the Benedictines, with which Thomas and his family had been previously associated. The story is that his parents had him kidnapped and locked away to try to dissuade him of his choice in religious orders. Yet Thomas was deeply committed to becoming a priest and, after a year in captivity, his mother arranged for him to “escape” through a window and he went on to join the Dominican order.

3. Thomas had a powerful vision that made him give up his writing career.

While saying mass one day, Aquinas experienced a mystical vision that was so powerful it made him view everything he had written as “straw worthy to be burned.” His vision of heavenly realities left him thinking that he could not adequately describe the profound mysteries revealed in Christian theology. Although his masterpiece Summa Theologiae consists of some two million words, he left it unfinished when he died at 49 years of age.

Even people who are familiar with his life and thought may not know of these three events. Aquinas’s achievements as a Christian scholar mark him as one of the most advanced thinkers of his time and the rationality of historic Christianity is in part demonstrated by the remarkable thinkers the faith has produced through the centuries. Yet, he was also a man who faced challenges and difficulties in his life just like all of us.

So, how about taking up his book Summa Theologiae? You’ll be reading a Christian classic as well as a masterwork of Western civilization.

Reflections: Your Turn

Which of the three points about Aquinas did you find most interesting? Visit Reflections on WordPress to comment.

Resources

For more about Thomas Aquinas and his accomplishments as a Christian thinker and writer, see Kenneth Richard Samples, Classic Christian Thinkers (Covina, CA: RTB Press, 2019), chapter 5.

Endnotes

1. G. K. Chesterton, Saint Thomas Aquinas: The Dumb Ox (New York: Doubleday, 1933).

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Farewell to the Forties
Farewell to the Forties

The decade that just slipped away without asking was the one where people––guys especially––thought they could still do stuff they did in their twenties….Theology

When Suffering Turns Your World Upside Down
When Suffering Turns Your World Upside Down

When you are young and healthy, it is easy to think that you are in control of your life and that you are the…Theology

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Does atheism have a true monopoly on reason? In my conversations with nonbelievers, I’ve found that probing deeper into the atheistic worldview exposes a key weakness in that perspective and provides an opportunity to demonstrate Christianity’s solid footing in reason. **** The heart has its reasons of which reason knows nothing. — Blaise Pascal, Pensées, 423/277. When I ask my unbelieving friends “Why are you an atheist?” they generally respond with something like “Because there is no God.” I ask them to dig a little deeper to answer my original question. Generally, a diatribe against religion emerges. Believers are accused of being a bunch of hypocrites who oppress people with their rules while religions are painted in broad strokes as ridiculous superstitions and crutches for weak-minded people. Many claim that belief in God is irrational. From my experience, the atheist asserts that humanity has evolved beyond these irrational impulses and structures, now seeing religion for the garbage it is. Why Atheism? My next question is, “Okay, but why choose atheism?” After all, a lack of faith comes with distinct disadvantages. For example, studies show that people with no faith are more likely than their religious counterparts to suffer from depression and to commit suicide.1 Besides that (or perhaps at the root of that), atheism doesn’t provide any sense of meaning or purpose for life because everything will end with total annihilation. Even if atheists argue that we can assign meaning to our lives, once the Sun burns out and the universe goes to heat death what is left? What will be the purpose of striving to not believe in superstition? What will be the purpose of helping other people? Why not just spend all your time throwing pebbles into the sea instead? In the end, such an activity will mean as much as the greatest acts of philanthropy. Pragmatically, wouldn’t it be better to be deluded and happy for this brief, meaningless time? Nonbelievers often answer that they choose atheism because it’s true. Further, pragmatism is not a good test for truth, which I concede. But is truth really worth possibly sacrificing health, happiness, and meaning? Here some opinions diverge, but most atheists would say that truth is of the utmost importance in dictating their worldview. “Alright,” I reply, “if truth is so important, why is it that only a small sliver of people ever find it?” My familiarity with scientists may bias this response, but I think most atheists would say that people believe in God because humanity has evolved to believe in God. In the past, religion served a useful function in promoting survival by bringing order to communities and existential motivation to mankind. Thus, over 90 percent of the world population today suffers from the effects of this grand evolutionary delusion. Only the free-thinkers, the “brights,” have figured out how to get beyond the rubbish of mysticism programmed into our genes through the evolutionary process. But if it’s true that the human brain is wired to believe in something that is false, then the brain is demonstrably unreliable for discerning truth. How then can atheists trust that their brain has found the truth? Why are they free from the mental subroutines programmed via evolution? How can they be certain that their brain finds truth, not just in this case, but ever? As recently highlighted by Kenneth Samples, atheism’s very assumptions about the world guarantee that we cannot know truth. We have become prisoners of our brain and the evolutionary processes that built it. Reason has been reduced to a molecular pool game with proteins and chemicals whacking about through neural circuitry, generating pictures, colors, and sensations. While having a molecular pool game governing your decisions may sound fun for a bit, it precludes any master-of-my-own-destiny claims to independence or ownership of achievements, capacities, or ideas. After all, you don’t own your ideas, choices, achievements or fate; that’s just the way the balls bounce. The Christian Alternative Bereft of the certainty of reason and truth that results from a godless worldview, it seems better for the atheist to seek an alternative. In his book C. S. Lewis’ Case for the Christian Faith, Richard Purtill offers the biblical perspective on reason and its origins (emphasis added): One way of getting a preliminary insight into Lewis’ argument [from reason] is to ask whether nature is a product of mind or mind is a product of nature. If God created nature, as Christians believe, then nature is understandable by reason because it is a product of reason.2 Christianity offers that man is made in the image of God and from this we gather that our mind is formed in likeness to God’s mind. Thus, we have a reason for our reason which is Jesus Christ, the creator of the universe, Earth, and our mind. Indeed the apostle John describes how “the Word” (logos, which can also be translated as “reason”) was with God in the beginning, how reason formed all of nature, and how the incarnate Word came to Earth. In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind.…The Word became flesh and made his dwelling among us. We have seen his glory, the glory of the one and only Son, who came from the Father, full of grace and truth. (John 1:1–4, 14) The idea of Christ as the Word is further refined in John 14:6 where Jesus describes Himself as “the way and the truth and the life.” Here Jesus, reason incarnate, properly claims primacy over truth and life, highlighting how truth and life flow from reason. Conversely, atheism fails to provide hope, a reason for living, a reason for meaning, or a reason for reason at all. With such a hopeless doctrine for life or truth, I hope atheists will consider reclaiming their reason by exploring the rich doctrines of Christianity that celebrate reason and hope.

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Thankful for Comets

 

Gazing upon the night sky during this holiday season may bring a glimpse of a comet that could put on an impressive display. Through Thanksgiving week, comet ISON (known as C/2012 S1 in more formal lingo) will head toward the Sun. If it survives the pass around the Sun without disintegrating, the comet may end up visible with the naked eye in through late December.

In my lifetime, only a handful of comets have grown bright enough to be detected without a telescope. The three most popular (at least as I remember) occurred during the 1990s.

My Top Three Comets

As impressive as ISON might appear, it won’t match the brilliance of comet Hyakutake (a.k.a. the Great Comet of 1996). I remember seeing this comet with the naked eye in March 1996, while working at the Fred Lawrence Whipple Observatory in southern Arizona. With clear, dark skies, I saw Hyakutake’s tail extending almost 90° across the starry expanse.

Image credit: Wikimedia/Creative Commons/E. Kolmhofer, H. Raab; Johannes-Kepler-Observatory, Linz, Austria (http://www.sternwarte.at)

Following closely on the tail (no pun intended) of Hyakutake, Hale-Bopp (the Great Comet of 1997) first appeared in the sky in May 1996. Its close passage to the Sun later that year made it difficult to see, but after showing up brilliantly again in January 1997, Hale-Bopp remained visible for the rest of the year.

Image credit: Wikimedia/Creative Commons/Michael K. Fairbanks

From a scientific perspective, the most interesting comet I’ve encountered is Shoemaker-Levy 9. Although this comet never brightened enough to be seen without a telescope, it made history in July 1994 when scientists observed its impact with Jupiter—making it the first collision between two large solar system bodies ever witnessed. On a previous trip close to Jupiter, Shoemaker-Levy 9 was ripped into 20+ pieces ranging in sizes of up to two kilometers in diameter. If a fragment of this size were to collide with Earth, the impact would release far more energy than the simultaneous detonation of the world’s entire nuclear arsenal!

Image credit: NASAESA, and H. Weaver and E. Smith (STScI)

Reasons to Be Thankful for Comets

Comets and asteroids impact our planet regularly—at least on geological timescales. While these impacts can cause great destruction (such as the impact that wiped out the dinosaurs), they also bring water and other important materials to Earth. Some collisions, like those during the Late Heavy Bombardment, helped prepare Earth for the next advance in its capacity to support life. One of the largest collisions in Earth’s history ultimately led to the formation of the Moon.

So, not only do comets provide spectacular displays in the heavens, they also play an important role in Earth’s habitability. As we (hopefully) glimpse comet ISON in the night sky, let’s thank God for so carefully crafting this planet as our home. (JZ,RTB)

*** Will Myers

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POSITIVE versus NEGATIVE STRESS

POSITIVE versus NEGATIVE STRESS – written by Dr Caroline Leaf
We have been told stress is always detrimental to our bodies. Not so! There is such a thing as positive stress!

Let me explain. Stress is the bodies reaction influences coming from outside or inside the body. Stress has three stages. Stage One is positive. In this stage we become alert and focused to the task at hand. This is normal. It is a temporary state.

Stage Two and Three, however, are negative. In Stage Two, the Stress Response is prolonged. Hormones like cortisol, which are only supposed to be increased for a short time, persist at high levels in the blood stream causing damage to our brains and bodies. If Stage Two becomes chronic and is maintained for a longer period it becomes Stage Three. At this point the body’s resources are exhausted, leading to disease and even death.

So what is the key to staying in positive and out of negative stress? It is our thought life, it is how we think. Research has shown that how we think about stress can affect whether we live or die.

The emerging fields medical specialities of psychoneuroendocrinology and psychoneuroimmunology are shedding light on the how thinking affects stress, the brain, the immune system and hormones and how these things determine our psychological and physical wellbeing. See my scientific-philosophy link (under ‘Thinking Affects Health’) for more on the science. Because Mind controls Matter, therefore, thinking is the pre-eminent influence on health. In fact 78% to 98% of the illnesses that plague us today are a direct result of our thought life.

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Twisted Evidence for Early Life

Anyone working on a home improvement project knows how important it is to have “the right tool for the right job.” This maxim also applies to science. Scientists need the right scientific tools if they ever hope to advance our understanding of the natural world. Perhaps no group of scientists has a greater need for the right tool than those exploring life’s origin and early history. Thankfully, help is on the way. Recent work by researchers from Germany and Switzerland describes a new tool that may help origin-of-life researchers finally identify fossils of the first life-forms.1

Earth’s oldest rock formations, located in western Greenland, date to 3.8 billion years in age. These rocks contain geochemical signatures that suggest life was present very early in the planet’s history—as soon as life support was even remotely possible.2 (For more details, check out the article, “When Did Life First Appear on Earth?”). Controversy accompanies the implications of these findings. Some researchers believe that these geochemical signatures may not reflect biological activity of first life. Instead, they argue, these features are due to abiotic processes that masquerade as biosignatures. To put it another way, geochemical markers aren’t necessarily the right tools to detect and characterize earliest life unambiguously.

If researchers could recover fossils of the first life-forms from the oldest rocks, it would go a long way toward demonstrating that life existed on Earth 3.8 billion years ago. Unfortunately, the rock formations of western Greenland have experienced extensive metamorphosis. High temperatures and pressures accompany these geological changes. These extreme conditions would have destroyed any fossils existing in the rocks.

Yet the researchers from Germany and Switzerland may have found a way, in principle, to detect fossils in these rock formations. Certain bacteria (microaerophilic Fe(II)-oxidizing bacteria) produce twisted stalk-like structures in the presence of high iron levels and low oxygen concentrations. The twisted stalks are formed from microbial secretions that then interact with iron minerals. These interactions stabilize the stalks. The researchers found these twisted structures in microbial mats recovered from a silver mine located in the Black Forest of Germany. When they subjected the microbial mats to high temperatures and pressures in the lab, the twisted stalks remained intact.

This exciting result suggests that it might be possible to recover twisted stalk fossils in the rock formations of Greenland. Twisted stalk structures have been observed in materials taken from rock formations that date to about 1.9 billion years in age. Early Earth’s oceans would have been loaded with iron in the form of Fe(II) and would have had low levels of oxygen. If microbes existed that could oxidize Fe(II), they would have likely produced twisted stalk structures. And if they did, then these structures have survived even if the rocks experienced extensive metamorphosis.

Unequivocal demonstration of life on Earth at 3.8 billion years ago would powerfully affirm RTB’s origin-of-life creation model. Our model predicts that life appeared soon after the planet’s formation. Meanwhile, an early appearance is unanticipated from an evolutionary perspective.

Will researchers be able to use this new tool to detect fossil evidence for life at 3.8 billion years ago? It is not clear yet—but the possibility puts RTB in a position to perform a definitive test of our creation model for life’s origin.

Subjects: First Life on Earth

Dr. Fazale Rana

In 1999, I left my position in R&D at a Fortune 500 company to join Reasons to Believe because I felt the most important thing I could do as a scientist is to communicate to skeptics and believers alike the powerful scientific evidence—evidence that is being uncovered day after day—for God’s existence and the reliability of Scripture. Read more about Dr. Fazale Rana

References:

  1. Aude Picard et al., “Experimental Diagenesis of Organo-Mineral Structures Formed by Microaerophilic Fe(II)-Oxidizing Bacteria,” Nature Communications 6 (February 18, 2015): id. 6277.
  2. Researchers believe that the first life-forms on Earth resembled contemporary bacteria and archaea.
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Evangelistic Guide; Witnessing Existence of God

In talking with a nontheist, have you ever felt like they expected you to know everything about even the most far-fetched theories—and if you didn’t, the evidence you did present was worthless?
It’s a growing problem in apologetics. Frankly, the evidence for the God of the Bible has grown so great today that nontheists are forced to appeal to what we do not know or cannot possibly know (called “nonempirical arguments”). Here are 3 tips you can start using today to reframe the discussion and avoid falling into the trap!
1. Question assumptions. The authors of a recent scientific paper declared they had shown that the universe has no beginning (and, therefore, no implied Beginner). They described the cosmic surface with “Bohmian trajectories.” They neglected to mention that Bohmian trajectories, by definition, disallow the possibility of singularities or beginnings. Their claim was based on circular reasoning. Always ask yourself: Are there unstated or unfounded assumptions here?
2. Focus on practical proof. Because of human limitations, absolute proof is simply beyond us. I have been married to Kathy for 39 years and all practical proofs demonstrate to me that she exists. Those proofs grow in number and strength every year. And yet there is still the faint possibility (mathematically) that she is a sophisticated hologram or complex illusion. Although I lack absolute proof, the practical proof is sufficient for me to commit myself to her until death. It is illogical to demand that God’s existence requires absolute proof.
3. Do an absurdity test. The question behind any theory is this: Do the processes that explain the theory become more or less rational as new evidence accumulates? Believe it or not, there are still vigorous flat-earth proponents out there. However, as our knowledge of the universe has grown, the explanations flat-earth proponents have been forced to invent have become ever more absurd. The nonempirical arguments being advanced by many nontheists today are also becoming increasingly strained to the point of absurdity.
Thanks to the gifts of dedicated people like you, RTB is always here to help you explore the latest scientific discoveries. We’re also here to help you see that every question and challenge can be an opportunity to invite people into a closer relationship with Jesus Christ. Will you make a gift now to help RTB continue providing the answers you and many other people count on?
Blog Summary and Highlights
Early agricultural industry. Biological convergence of unrelated organisms. America’s founding fathers. At first glance, these topics have no outward similarities. This week, however, our scholars shared their insights on these issues and more to show how God’s timing, design, and hand in history displays his purpose for humanity. Check out the RTB scholar blogs for more!
Farming Revolution Simultaneously Launches in Multiple Locations” by Hugh Ross
Like a Fish Out of Water: Why I’m Skeptical of the Evolutionary Paradigm” by Fazale Rana
How a Christian Worldview Influenced America’s Founding Fathers” by Andrew Stebbins
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Did Neanderthals Start Fires?

BY FAZALE RANA – DECEMBER 5, 2018

It is one of the most iconic Christmas songs of all time.

Written by Bob Wells and Mel Torme in the summer of 1945, “The Christmas Song” (subtitled “Chestnuts Roasting on an Open Fire”) was crafted in less than an hour. As the story goes, Wells and Torme were trying to stay cool during the blistering summer heat by thinking cool thoughts and then jotting them down on paper. And, in the process, “The Christmas Song” was born.

Many of the song’s lyrics evoke images of winter, particularly around Christmastime. But none has come to exemplify the quiet peace of a Christmas evening more than the song’s first line, “Chestnuts roasting on an open fire . . . ”

Gathering around the fire to stay warm, to cook food, and to share in a community has been an integral part of the human experience throughout history—including human prehistory. Most certainly our ability to master fire played a role in our survival as a species and in our ability as human beings to occupy and thrive in some of the world’s coldest, harshest climates.

But fire use is not limited only to modern humans. There is strong evidence that Neanderthals made use of fire. But, did these creatures have control over fire in the same way we do? In other words, did Neanderthals master fire? Or, did they merely make opportunistic use of natural fires? These questions are hotly debated by anthropologists today and they contribute to a broader discussion about the cognitive capacity of Neanderthals. Part of that discussion includes whether these creatures were cognitively inferior to us or whether they were our intellectual equals.

In an attempt to answer these questions, a team of researchers from the Netherlands and France characterized the microwear patterns on bifacial (having opposite sides that have been worked on to form an edge) tools made from flint recovered from Neanderthal sites, and concluded that the wear patterns suggest that these hominins used pyrite to repeatedly strike the flint. This process generates sparks that can be used to start fires.1 To put it another way, the researchers concluded that Neanderthals had mastery over fire because they knew how to start fires.

blog__inline--did-neanderthals-start-fires-1

Figure 1: Biface tools for cutting or scraping. Image credit: Shutterstock

However, a closer examination of the evidence along with results of other studies, including recent insight into the cause of Neanderthal extinction, raises significant doubts about this conclusion.

What Do the Microwear Patterns on Flint Say?

The investigators focused on the microwear patterns of flint bifaces recovered from Neanderthal sites as a marker for fire mastery because of the well-known practice among hunter-gatherers and pastoralists of striking flint with pyrite (an iron disulfide mineral) to generate sparks to start fires. Presumably, the first modern humans also used this technique to start fires.

blog__inline--did-neanderthals-start-fires-2

Figure 2: Starting a fire with pyrite and flint. Image credit: Shutterstock

The research team reasoned that if Neanderthals started fires, they would use a similar tactic. Careful examination of the microwear patterns on the bifaces led the research team to conclude that these tools were repeatedly struck by hard materials, with the strikes all occurring in the same direction along the bifaces’ long axis.

The researchers then tried to experimentally recreate the microwear pattern in a laboratory setting. To do so, they struck biface replicas with a number of different types of materials, including pyrites, and concluded that the patterns produced by the pyrite strikes most closely matched the patterns on the bifaces recovered from Neanderthal sites. On this basis, the researchers claim that they have found evidence that Neanderthals deliberately started fires.

Did Neanderthals Master Fire?

While this conclusion is possible, at best this study provides circumstantial, not direct, evidence for Neanderthal mastery of fire. In fact, other evidence counts against this conclusion. For example, bifaces with the same type of microwear patterns have been found at other Neanderthal sites, locales that show no evidence of fire use. These bifaces would have had a range of usages, including butchery of the remains of dead animals. So, it is possible that these tools were never used to start fires—even at sites with evidence for fire usage.

Another challenge to the conclusion comes from the failure to detect any pyrite on the bifaces recovered from the Neanderthal sites. Flint recovered from modern human sites shows visible evidence of pyrite. And yet the research team failed to detect even trace amounts of pyrite on the Neanderthal bifaces during the course of their microanalysis.

This observation raises further doubt about whether the flint from the Neanderthal sites was used as a fire starter tool. Rather, it points to the possibility that Neanderthals struck the bifaces with materials other than pyrite for reasons not yet understood.

The conclusion that Neanderthals mastered fire also does not square with results from other studies. For example, a careful assessment of archaeological sites in southern France occupied by Neanderthals from about 100,000 to 40,000 years ago indicates that Neanderthals could not create fire. Instead, these hominins made opportunistic use of natural fire when it was available to them.2

These French sites do show clear evidence of Neanderthal fire use, but when researchers correlated the archaeological layers displaying evidence for fire use with the paleoclimate data, they found an unexpected pattern. Neanderthals used fire during warm climate conditions and failed to use fire during cold periods—the opposite of what would be predicted if Neanderthals had mastered fire.

Lightning strikes that would generate natural fires are much more likely to occur during warm periods. Instead of creating fire, Neanderthals most likely harnessed natural fire and cultivated it as long as they could before it extinguished.

Another study also raises questions about the ability of Neanderthals to start fires.3 This research indicates that cold climates triggered Neanderthal extinctions. By studying the chemical composition of stalagmites in two Romanian caves, an international research team concluded that there were two prolonged and extremely cold periods between 44,000 and 40,000 years ago. (The chemical composition of stalagmites varies with temperature.)

The researchers also noted that during these cold periods, the archaeological record for Neanderthals disappears. They interpret this disappearance to reflect a dramatic reduction in Neanderthal population numbers. Researchers speculate that when this population downturn took place during the first cold period, modern humans made their way into Europe. Being better suited for survival in the cold climate, modern human numbers increased. When the cold climate mitigated, Neanderthals were unable to recover their numbers because of the growing populations of modern humans in Europe. Presumably, after the second cold period, Neanderthal numbers dropped to the point that they couldn’t recover, and hence, became extinct.

But why would modern humans be more capable than Neanderthals of surviving under extremely cold conditions? It seems as if it should be the other way around. Neanderthals had a hyper-polar body design that made them ideally suited to withstand cold conditions. Neanderthal bodies were stout and compact, comprised of barrel-shaped torsos and shorter limbs, which helped them retain body heat. Their noses were long and sinus cavities extensive, which helped them warm the cold air they breathed before it reached their lungs. But, despite this advantage, Neanderthals died out and modern humans thrived.

Some anthropologists believe that the survival discrepancy could be due to dietary differences. Some data indicates that modern humans had a more varied diet than Neanderthals. Presumably, these creatures primarily consumed large herbivores—animals that disappeared when the climatic conditions turned cold, thereby threatening Neanderthal survival. On the other hand, modern humans were able to adjust to the cold conditions by shifting their diets.

But could there be a different explanation? Could it be that with their mastery of fire, modern humans were able to survive cold conditions? And did Neanderthals die out because they could not start fires?

Taken in its entirety, the data seems to indicate that Neanderthals lacked mastery of fire but could use it opportunistically. And, in a broader context, the data indicates that Neanderthals were cognitively inferior to humans.

What Difference Does It Make?

One of the most important ideas taught in Scripture is that human beings uniquely bear God’s image. As such, every human being has immeasurable worth and value. And because we bear God’s image, we can enter into a relationship with our Maker.

However, if Neanderthals possessed advanced cognitive ability just like that of modern humans, then it becomes difficult to maintain the view that modern humans are unique and exceptional. If human beings aren’t exceptional, then it becomes a challenge to defend the idea that human beings are made in God’s image.

Yet, claims that Neanderthals are cognitive equals to modern humans fail to withstand scientific scrutiny, time and time, again. Now it’s time to light a fire in my fireplace and enjoy a few contemplative moments thinking about the real meaning of Christmas.

Resources

Endnotes
  1. A. C. Sorensen, E. Claud, and M. Soressi, “Neanderthal Fire-Making Technology Inferred from Microwear Analysis,” Scientific Reports 8 (July 19, 2018): 10065, doi:10.1038/s41598-018-28342-9.
  2. Dennis M. Sandgathe et al., “Timing of the Appearance of Habitual Fire Use,” Proceedings of the National Academy of Sciences, USA 108 (July 19, 2011), E298, doi:10.1073/pnas.1106759108; Paul Goldberg et al., “New Evidence on Neandertal Use of Fire: Examples from Roc de Marsal and Pech de l’Azé IV,” Quaternary International 247 (2012): 325–40, doi:10.1016/j.quaint.2010.11.015; Dennis M. Sandgathe et al., “On the Role of Fire in Neandertal Adaptations in Western Europe: Evidence from Pech de l’Azé IV and Roc de Marsal, France,” PaleoAnthropology (2011): 216–42, doi:10.4207/PA.2011.ART54.
  3. Michael Staubwasser et al., “Impact of Climate Change on the Transition of Neanderthals to Modern Humans in Europe,” Proceedings of the National Academy of Sciences, USA 115 (September 11, 2018): 9116–21, doi:10.1073/pnas.1808647115.

About Reasons to Believe

RTB’s mission is to spread the Christian Gospel by demonstrating that sound reason and scientific research—including the very latest discoveries—consistently support, rather than erode, confidence in the truth of the Bible and faith in the personal, transcendent God revealed in both Scripture and nature. Learn More »

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