Today’s New Reason To Believe

David H. Rogstad, Ph.D.

In my study of Scripture I occasionally come across a passage that captures my attention because it encapsulates a particular idea in a complete way. Examples that immediately come to mind are Psalms 1 where we find clear steps describing how to have success in all we do, or Titus 2:11-14 where we learn of the work that grace is accomplishing in our lives. Another passage that has been especially meaningful to me over the years is Paul’s comments to Timothy found in 1 Timothy 1:5:

But the goal of our instruction is love from a pure heart and a good conscience and a sincere faith. (NASB)

What I hear Paul saying is that, in the end, his entire ministry is driving toward one all-important goal, which is for us to fully experience God’s rich and abundant love. All of his teaching, reproof, correction, and training in righteousness (2 Timothy 3:16) is intended bring us to that end. Even the ministry of apologetics that we do here at Reasons To Believe holds the experience of God’s love as its goal.

However, in this passage he also gives us some qualifications on our experience of God’s love that are essential for us to receive and display it in its fullness. As I have meditated on this passage, the picture I have in my mind is that God’s love is like a fountain springing forth from our lives as we enter into the salvation He has provided in Christ. But unless we reflect in our lives the three characteristics Paul mentions, there is a danger that the fountain of His love will be tainted. The challenge to me, then, is, by God’s grace, to develop a pure heart, a clear conscience, and a genuine faith.

My heart is pure if I am free from anger and bitterness because of a willingness to practice forgiveness toward those who offend me; and I am free from moral impurity as I flee from temptation by taking steps to rid myself of thoughts and actions that will defile my spirit. In today’s world we are bombarded from every direction with images and reading material that sullies our minds. In this area, I have had to take very deliberate and sometimes painful steps to guard my heart from moral failure.

I develop a clear conscience when I am willing to take responsibility for the sin in my life rather than blaming others. This involves asking forgiveness of those I have offended, and making restitution when necessary. For me, this has involved making a list and, with great resolve, returning to those I have trespassed against, asking their forgiveness, and paying for things I have stolen. My children testify that one of the most important ways I gained their respect while growing up was through my willingness to ask their forgiveness when I falsely accused or over-disciplined them. All the pain and humiliation has been well worth the benefits gained from taking these steps.

Finally, I have sincere faith when I realize that, in the end, when all has been said and done, that God is right, His words are true, and His ways are perfect. We lose nothing and gain everything when we take His word at face value and determine in our hearts that we will believe it and apply it in our lives. The word “sincere” comes from the Latin and literally means “without wax.” A statue carved by a true artist was one that did not need mistakes to be filled in or covered over with wax. Sincere faith is the faith of a sinner that is willing to walk in the light, not hiding his faults but confessing them and experiencing the justifying and cleansing grace of God.

The end of this process, for it is a process, is a deeper experience of God’s love because it “has been poured within our hearts through the Holy Spirit who was given to us” (Romans 5:5). While our reasons to believe may affirm our faith, it is the work of the Holy Spirit and our response to it that brings us into a vital relationship with the God of creation.

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.

by Jeff Zweerink

I enjoy traveling, whether taking a trip to visit relatives for Christmas or a summertime vacation to witness the beauty of creation. However, any trip with my family (wife and five kids) requires lots of preparation in order to achieve success. Clothes must be packed, bills paid, lodging reserved, and the list goes on. These tasks must also be accomplished in the proper order. Trying to pack clothes after a trip begins is highly unadvisable. Likewise, when the solar system formed, certain events needed to take place before others in order to establish a life-friendly cosmic habitat.

As described in Rare Earth, advanced life depends on plate tectonics. In order for a planet as small as Earth to experience long-standing plate tectonics, it must have a large supply of radioactive nuclei that will emit the heat that drives tectonic activity. These nuclei form in the massive supernova explosions that occur as stars die. However, like packing for a trip, the nearby supernovae that seed the planets with radioactive material must take place at the proper time. If they occur too early (or too close) the supernovae might blow the solar nebula apart and prevent the formation of the solar system. If they occur too late, the planets will have already formed without incorporating the necessary radioactive elements. I have detailed some of the evidence about this fine-tuning in a previous TNRTB.

Astronomers and geophysicists have discovered evidence of such “fine-timing” by looking at meteorites that formed in the early solar system and recently landed on Earth. Some of these meteorites, known as chondrites, record the conditions present in the early solar system because they have not been melted or otherwise processed since their formation. They include different components such as calcium-aluminum inclusions (CAIs) and chondrules. According to most models that incorporate finely timed supernova explosions in the early solar system, these components form at different times. In particular, the chondrules should form later than the CAIs.

The research measured ages of the chondrules at 1.66 million years younger than the CAIs. This number supports models where the aluminum enters the solar nebula shortly after a nearby supernova explosion occurs. It also provides further evidence that the solar system formed between 4.57 and 4.56 billion years ago. The proper timing of events in the early solar system ensured that Earth had all the necessary “clothes” so that the life-essential plate tectonics would continue for the duration of Earth’s trip through this universe.