Today’s New Reason To Believe

Posted by Fazale ‘Fuz’ Rana, Ph.D.

New Insight into the Cell’s Quality-Control Systems Provided Added Evidence for Design

Have you ever had trash that the garbage man wouldn’t take? We sure have.

I remember a few years ago we re-carpeted the upstairs of our home. Instead of having the carpet layers take the left over remnants with them when they finished the job, we decided to save the carpet scraps—just in case. Big mistake!

After spending several months tripping over the rolls of carpet in our garage, we decided to throw them away. First, we naively dragged the carpet to the curb and set it next to our trash barrels. The trash men refused to take it. The next week, we took great pains to fit the carpet into the appropriate trash barrel, only to have it removed by the trash collectors and left unceremoniously on the curbside. I don’t remember how we finally got rid of the carpet, but I do remember the valuable lesson we learned about trash disposal and what the garbage man will and won’t take.

Cells face similar problems when it comes to disposing biochemical trash. Some cellular garbage is readily cleared from the cell. Other biomolecular refuse, like carpet remnants, is difficult for the cell’s machinery to process. This difficulty causes biochemical waste to accumulate in the cell’s interior.

Accumulating cellular garbage is not a matter of inconvenience, like the unwanted carpet stacked in my garage. It’s a real concern. In fact, part of the etiology of some neurodegenerative disorders, like Huntington’s Disease, involves the build-up of aggregates formed from protein waste.

Understandably, biologists are interested in trying to learn how and why protein waste accumulates in cells and what can be done to eliminate it. New work published in Nature provides important insight into how protein waste is processed by the cell. This new knowledge suggests a possible strategy to help cells clear out intractable biomolecular garbage. This new understanding also adds to the evidence that life stems from a Creator’s hand.

Next week I’ll discuss these ideas. This week I’ll describe what makes up a major part of the cell’s garbage and the central cogs in the cell’s waste disposal machinery.

Proteins

The cell’s waste, like most garbage, doesn’t start out that way. Initially, it is useful. Much of the offending cellular rubbish consists of protein aggregates. Proteins are chain-like molecules that fold into precise three-dimensional structures. A protein’s three-dimensional architecture determines its function. Proteins play a key role in virtually every cellular function and help form nearly every cellular structure.

Proteins form when the cellular machinery links together, in a head-to-tail fashion, smaller subunit molecules called amino acids. The amino acids that make up the cell’s protein chains possess a variety of chemical and physical properties. Each amino acid sequence imparts the protein with a unique chemical and physical profile along its chain. This profile determines how the protein folds, and therefore, how it interacts with other protein chains to form functional protein complexes. The amino acid sequence of a protein ultimately determines its function, since the amino acid sequence determines the protein’s structure, and hence, structure dictates function.

Protein Waste

Cells constantly make and destroy proteins. Proteins that take part only in highly specialized activities within the cell are manufactured only when needed. Once these proteins outlive their usefulness, the cell breaks them down into their constitutive amino acids. The removal of unnecessary proteins helps keep the cell’s interior free of clutter. And the amino acids can be used to build new proteins.

On the other hand, proteins that play a central role in the cell’s operation are produced on a continual basis. After a period of time, however, these proteins inevitably suffer damage from wear and tear and must be destroyed and replaced with newly made proteins. It’s dangerous for the cell to let damaged proteins linger. Once a protein is damaged, it’s prone to aggregate with other proteins. These aggregates disrupt cellular activities.

Another source of protein waste is faulty manufacturing. The assembly of protein chains from constitutive amino acids occurs with a high degree of fidelity. However, the folding of the protein chains into their native three-dimensional architecture is still error-prone. The error rate is typically about thirty percent. (As I point out in The Cell’s Design and elsewhere, this high error rate represents an elegant design strategy to ward off viruses.)

Misfolded proteins can cause profound problems for the cell. The negative consequences of their presence extend beyond loss of function for the misfolded protein. Improperly folded proteins have a global impact on cellular health. These deformed proteins tend to form aggregates inside the cell, fouling up its inner workings.

Fortunately, the cell possesses protein degradation machinery that clears unneeded, damaged, and improperly manufactured proteins.

Protein Disposal

Protein degradation is a complex undertaking that begins with what biochemists call ubiquitination. When damaged, proteins misfold adopting a nonnatural three-dimensional shape. Misfolding exposes amino acids in the damaged protein’s interior. These exposed amino acids are recognized by an enzyme called E3 ubiquitin ligase, which attaches a small protein molecule called ubiquitin to the damaged protein.

Ubiquitin functions as a molecular tag, informing the cell’s machinery that the damaged protein is to be destroyed. Severely damaged proteins will receive multiple ubiquitin tags. Ubiquitination is reversible by deubiquitinating enzymes removing the ubquitin labels. This deubiquitinating activity prevents the cell’s machinery from breaking down fully functional proteins that may have been accidentally tagged for destruction.

A massive protein complex called a proteasome destroys damaged, ubiquitinated proteins. The overall molecular architecture of the proteasome consists of a hollow cylinder topped with a lid that can exist in either an opened or closed conformation. Protein breakdown takes place within the cylinder’s interior. The lid portion of the proteasome controls the entry of ubiquitinated proteins into the cylinder.

As I point out in The Cell’s Design, the proteasome lid contains deubiquitinating activity. If a protein has only one or two ubiquitin tags, it’s likely not damaged and the lid will remove the tags thereby rescuing the protein from destruction. The cell’s machinery will recycle the rescued protein. If, on the other hand, the protein has several ubiquitin tags, the lid cannot remove them all and shuttles the damaged protein entry into the proteasome cylinder.

The proteasome lid regulates a delicate balance between destruction and rescue, ensuring that truly damaged proteins are destroyed and salvageable proteins escape unnecessary degradation. As I argue in The Cell’s Design, the cell’s protein degradation system displays fine-tuning and also elegant biochemical logic that points to a Creator’s handiwork.

High-precision equates with the best possible quality in engineered systems. Precision and fine-tuning do not arise by happenstance in either art or engineering. Rather, they come about only as a result of careful planning and a commitment to execute designs using the best craftsmanship possible. This makes fine-tuning and precision clear indicators of human intelligent design. And, by analogy, makes the molecular precision and fine-tuning that pervades the design of biochemical systems potent markers for the work of a Divine Engineer.

David H. Rogstad, Ph.D.

I just finished reading a book that has been on my shelf for some time. It is William Lane Craig’s apologetic for the Christian faith entitled Reasonable Faith: Christian Truth and Apologetics (This is actually a newly published 3rd edition; I read the 2nd edition). It sat there as long as it did because I had the impression it would not be an easy read. I was right. But upon my perusal, it proved to be a rich source of material on a variety of apologetic topics. The summaries that he added to the end of each chapter are particularly helpful, giving suggestions to the reader on how to make use of the arguments presented.

Two sections in particular caught my attention. The first (found toward the end chapter 1) was his discussion of the self-authenticating witness of the Holy Spirit in the life of the believer. It is unusual for a book this intently intellectual to call attention to this (in my view) most important argument for our faith. The second section (in chapter two) was his discussion of the absurdity of a life without God.

He opens this chapter summarizing the comments of a number of authors, including Pascal, Dostoyevsky, Kierkegaard, and Schaeffer, who have written about the “human predicament” of a life without God. All of these authors addressed the despair humanity faces in such circumstances.

Then Craig begins his assessment of what the human predicament entails: “If God does not exist, then both man and the universe are inevitably doomed to death.” Life has no ultimate meaning, value, or purpose. As he expands on each of these areas, he paints a grim picture of life without immortality and God. To communicate the power of his style, I quote from the text.

On meaning he says:

If each individual person passes out of existence when he dies, then what ultimate meaning can be given to his life? Does it really matter whether he ever existed at all? It might be said that his life was important because it influenced others or affected the course of history. But this shows only a relative significance to his life, not an ultimate significance.

On value:

If life ends at the grave, then it makes no difference whether one has lived as a Stalin or as a saint. Since one’s destiny is ultimately unrelated to one’s behavior, you may as well just live as you please…In a world without a divine lawgiver, there can be no objective right and wrong, only our culturally and personally relative, subjective judgments.

On purpose:

If death stands with open arms at the end of life’s trail, then what is the goal of life? To what end has life been lived?…Is it utterly pointless? If its destiny is a cold grave in the recesses of outer space, the answer must be yes—it is pointless. There is no goal, no purpose, for the universe…If there is no God, then our life is not fundamentally different from that of a dog.

In the closing sections of his chapter, Craig then addresses the practical impossibility of living, consistently, a life of atheism, and at the same time, to remain happy. It is either one or the other. Philosophers will say, in the face of this dilemma, we should create meaning by following a chosen course of action. But how can we, on the one hand, believe life is absurd, and on the other, try to create meaning? It makes no sense. It is a game of pretense. How can a person be a social critic, like Bertrand Russell, denouncing war and restrictions on sexual freedom, and at the same time admit that these things are just a matter of personal taste? If there is not God, then all the evil acts of men go unpunished and all the sacrifices of good men go unrewarded. Who can live with such a view? Craig argues that many who live a life of atheism, in fact, subconsciously borrow belief in immortality from those who held to it in the past. But they have no ground for believing now. In summary, he says:

Man cannot live consistently and happily as though life were ultimately without meaning, value, or purpose. If we try to live consistently within the framework of the atheistic worldview, we shall find ourselves profoundly unhappy. If instead we manage to live happily, it is only by giving the lie to our worldview.

Craig then points out that if the Christian worldview is correct, God does exist, life does not end with the grave, and we do have meaning, value, and purpose. Because of this, we can live both a consistent and a happy life!

Altogether, I find his discussion provides a powerful apologetic for biblical Christianity.

New insight into the origin of agriculture buttresses a weak spot in RTB’s human origins model.

All scientific models have weaknesses. RTB’s creation model is no exception. Even though the RTB human origins model finds powerful support from the scientific record, there is some unease related to the origin of agriculture. Recent discoveries—recounted in an article written by science journalist Michael Balter—help alleviate some of this discomfort.

The RTB model maintains that:

1. Humanity traces back to a single woman and a single man.
2. Humanity’s original population size was relatively small.
3. Humanity originates in a single location at or near the Middle East.
4. Humanity’s origin dates back to between 10,000 to 100,000 years ago.
5. Humanity spread around the world, recently, from near the Middle East.

Studies on the genetic diversity of people groups from around the world are provocative in light of the RTB model. This work indicates that modern humans originated at a single location (at or near the presumed site of the Garden of Eden), recently (less than 100,000 years ago), and from a small initial population that traces back to a single man and woman. The archeological and genetic evidence shows that by 50,000 to 60,000 years ago humans had spread from near the Middle East into Asia and Europe with a migration pattern that fits with the biblical text. For details see Who Was Adam?

Even though the genetic data powerfully affirms the biblical description of humanity’s origin, some are troubled by the dates for humanity’s origin and spread in light of the timing of agriculture’s appearance. The scientific evidence indicates that wide-scale agricultural practices emerged around 10,000 years ago—well after humanity’s origin and migration around the world.

In contrast, the RTB model predicts that some type of farming and animal husbandry were in use close to the time of humanity’s beginning. Genesis 4:1-4 teaches that Adam and Eve’s sons, Cain and Abel, “worked the soil” and “kept flocks,” respectively. This model also maintains that farming and animal husbandry spread from the Middle East to different locations around the world as a consequence of human migrations.

On the surface, the scientific evidence seems to contradict the RTB human origins model.

This discrepancy can be resolved if the archeological and genetic evidence traces the origin of the large-scale domestication of plants and animals, not the origin of agriculture itself. It’s possible that the first humans engaged in farming and animal husbandry well before 10,000 years ago at levels that escape scientific detection. Accordingly, the first humans lived as hunter-gathers, but they supplemented this lifestyle by harvesting and manipulating wild plants and taming wild animals.

The latest understanding of agriculture’s origin supports this assertion. Studies of the Ohalo II site in Israel indicate that humans were engaged in proto-farming practices nearly 12,000 years before the Neolithic revolution. Field evidence suggests that the domestication of plants was a gradual process, occurring over the course of several thousand years. Humans cultivated wild plants for thousands of years before the plants showed the anatomical changes associated with domestication. Once domesticated plants were developed, they were planted in mixed fields along with wild versions of the crop.

New evidence also indicates that domestication occurred independently around the world about 10 separate times. The first large-scale domestication of plants occurred about 13,000 years ago in the Fertile Crescent, followed by domestication activities in Southeast Asia and New Guinea 8,000 and 7,000 years ago, respectively. Recent studies have even uncovered evidence for large-scale plant domestication in South America as far back as 10,000 years ago, only a few thousand years after the first humans made their way into the Americas.

The independent, multiple origins of large-scale agriculture support the notion that the first humans engaged in farming and animal husbandry well before 12,000 years ago. It seems highly unlikely that human beings would have independently and simultaneously discovered plant and animal domestication that many times. It appears as if humans took with them a well-developed understanding of farming and animal husbandry when they migrated to different regions of the world.

In the context of the RTB human origins model, these new insights into the origin of agriculture suggest that Cain and Abel were engaged in proto-farming and proto-husbandry.