Reasons to Believe

Connections 2007, Vol. 9, No. 3



The Genetic Code: Simply the Best
Fazale (Fuz) R. Rana, Ph.D.

What was the best movie of the past year? Who is the best-dressed celebrity? What is the best university in the country? Many people are fascinated by lists of “the best.” And apologetics is no exception.

I am often asked what I think to be the best argument for intelligent design. From my vantage point as a biochemist, it's the genetic code. Recently published research adds to my conviction.

The genetic code resides at the heart of the cell’s chemistry. This code-universal to all organisms (at least to a first approximation)-consists of a set of rules. The cell's machinery uses these rules to convert the information stored in DNA into the information functionally expressed in proteins.

The Information Chain
Proteins-the "workhorse" molecules of life-take part in essentially every cellular and extracellular structure and activity. Proteins are chain-like molecules that fold into precise three-dimensional structures. And these structures determine each protein’s function. The molecular chains of proteins form when the cell’s machinery links together smaller molecules called amino acids. The specific sequence of amino acids dictates a protein's structure, and hence its function.

DNA houses the information the cell’s machinery uses to make proteins. DNA consists of two parallel molecular chains intertwined around one another in a helical fashion. The DNA strands are comprised of smaller molecules, called nucleotides, bound together like amino acids. The sequence of nucleotides signifies the amino acid sequences of proteins.

Experience teaches that intelligible messages-information-come from intelligent sources. A code requires someone to create it, and this common experience makes the genetic code a potent indicator of intelligent design. (See "What is a Code?" on page 8.)

So too does the genetic code's capacity to withstand errors caused by mutations. Even though mutations are potentially harmful, the rules that define the genetic code appear to be carefully constructed to minimize these errors. In fact, research indicates that the universal genetic code has a better error-minimization capacity than virtually any other conceivable set of rules that could have been used to construct the genetic code. Such radical optimization epitomizes intelligent design.

It doesn’t stop there. Recent work indicates that DNA harbors additional codes that overlay the genetic code. These codes consist of rules that independently direct the binding of histone proteins and transcription factors to DNA and dictate processes like messenger RNA folding and splicing. These code-driven critical activities regulate protein production. Again, a code requires a mind to create it. And multiple overlapping codes require a mind to structure them in such a way that they work in conjunction-instead of interfering-with one another. As if this evidence wasn't enough, another new study shows that the genetic code is also optimized to harbor the overlapping codes.

One study demonstrated that the co-expression patterns of genes for humans and chimpanzees differ considerably in the cerebral cortex but are largely similar in subcortical regions.2 Another study indicates that human and chimp genomes vary in microRNA (molecules that regulate gene expression) content.3 The way genes are regulated and expressed corresponds to the profound dissimilarities in human and chimpanzee brain structures and cognitive abilities (behavior), thereby explaining the crucial differences between humans and the great apes.

This amazing, life-critical code likely won't make any top ten lists in popular culture, but when it comes to evidence for intelligent design, the genetic code found throughout nature is simply "the best".

References
1. Fazale Rana, “FYI: I.D. in DNA; Deciphering Design in the Genetic Code,”Facts for Faith, no. 8, first quarter 2002, 14-23.
2. Eran Segal et al., “A Genomic Code for Nucleosome Positioning,” Nature 442 (2006): 772-78
3. Shalev Itzkovitz and Uri Alon, “The Genetic Code Is Nearly Optimal for Allowing Additional Information within Protein-Coding Sequences,” Genome Research (2007): advanced online.

 


Buttressing the Distance Ladder Foundation for Cosmic Creation
Hugh Ross, Ph.D.

Not until Albert Einstein produced his theory of general relativity in 1916 did scientists even consider the possibility that the cosmos continually expands. And yet five ancient writers—Job, David, Isaiah, Jeremiah, and Zechariah—all described this expansion more than two thousand years ago.1 For centuries the Bible stood alone as the only text making such a claim about the universe. So today, as the body of evidence for continual expansion grows, the case for the reliability and predictive power of the Bible and of the Christian worldview also grows. A breakthrough from a team of American radio astronomers just added to it.

Until a few years ago, the most reliable measurements of the expansion rate of the universe relied on what’s called the “distance-ladder” method. (Even today, this method is still considered one of the pillars for determining the expansion history of the universe because it offers insights to the expansion rate at multiple cosmic epochs.) Using direct distance measurements to nearby objects, astronomers use indirect distance methods to extrapolate the distance to more-distant objects. The indirect methods make certain assumptions about the properties of the observed objects while the direct methods are assumption free.

Direct distance measurements rely upon the theorems taught in high school-level geometry classes. Traditionally, the diameter of Earth's orbit becomes the base of the triangle for these calculations. But because that base of 186 million miles is comparatively small (on an astronomical scale), the nearly perpendicular side angles and extremely narrow vertex angle of the triangle—think of a very long, narrow triangle—for stars located more than a thousand light-years distant seriously limit the precision of such measurements and thus the applicability of the method.

In recent months, however, an American radio astronomy team announced the completion of a three-year research project that vaulted measuring accuracy from distances of about a thousand light-years or less to a distance of 25 million light-years. With the help of NGC 4258 (a galaxy), they improved the accuracy by a factor of 25,000.2 Rather than using the diameter of Earth's orbit as the baseline of the distance-calculating triangle, they used the much larger baseline provided by a microwave laser, or “maser,” centered on a super-giant black hole in NGC 4258.

Because the astronomers are making use of radio wavelengths, they are able to electronically link radio telescopes all over the globe to create an instrument with an angular resolving power a thousand times greater than the biggest ground-based optical telescope in existence and a hundred times superior to the Hubble Space Telescope. The long-term integration over which observations of the maser are made allows for an additional hundredfold improvement in the accuracy of the measurements.

As a result of this project, the radio astronomy team has now accumulated the data to produce a direct distance measurement from Earth out to NGC 4258, one that’s accurate to about 5 percent precision (and to about 3 percent in subsequent observations). This accuracy more than doubles that of even the best among various indirect methods, regardless of the reliability of the assumptions on which they rest. Such accuracy will permit some important advances, including these two: (1) it will allow astronomers to test the validity of multiple assumptions underlying the indirect measuring methods; and (2) it will deliver double the quality and, therefore, twice the reliability of many of researchers’ earlier cosmic expansion measurements.

So far, the team has published their observations of the maser, their data reduction techniques, and the temporal and spatial characteristics of the maser. In a soon-to-be-published paper they will present their actual measurements of the distance to NGC 4258. Then we can all enjoy a more certain picture of the universe's expansion history and a more accurate calculation of the time back to the cosmic creation event—the event of which Moses wrote in Genesis 1:1.

References:

1. Hugh Ross, The Creator and the Cosmos, 3rd ed. (Colorado Springs: NavPress, 2001): 23-29.

2. A. L. Argon et al., “Toward a New Geometric Distance to the Active Galaxy NGC 4258. I. VLBI Monitoring of Water Maser Emission,” Astrophysical Journal 659 (April 20, 2007): 1040-62.



What is a Code?

David H. Rogstad, Ph.D

As kids we had great fun passing handwritten notes to each other across the classroom. The challenge was to avoid the teacher’s detection. The more "sophisticated" among us would convert them into secret messages by writing them in code. Unfortunately, the teacher was no dummy and easily figured out the code—each letter was a number, in sequence—and embarrassed us in front of the class by reading aloud our secret message.

Not until later as a science student did I learn of the broad application codes have in a variety of fields. Encryption codes, analogous to our crude grammar school attempts, have been used to send secret messages in times of war. This technology has found its way into everyday life in the sending of private emails, where the email program on our computer provides the encryption/decryption (translation) process. Another type, the Universal Product Code, consists of parallel lines of varying width and separation printed on merchandise that provide information about the product.

In computers, programmers write codes that act like recipes. The code instructs the computer to perform certain operations just like a recipe instructs a cook how to bake a cake. Computer programming can occur at two levels. There are high-level codes, written in programming languages like BASIC, that allow the programmer to "talk" to the computer in natural, English-like, phrases. These are translated by compilers into low-level codes written in languages specific to the particular computer processor being used.

The low-level computer codes are very cryptic in that they use short mnemonics to represent each particular operation. The three-letter mnemonics like ADD, SUB, MUL or DIV are obvious, but others like CMP (compare), CLR (clear a register), XOR (binary operation of "exclusive OR") are not. Each of these operations is then translated by an assembler into a sequence of zeros and ones (computers use the binary 0 and 1 system instead of the decimal 0 through 9 system to represent numbers), called the machine code, that the computer understands for performing operations. The particular set of zeros and ones used to define the machine code are carefully designed to ensure that all operations are properly encoded and the associated information that goes with the operation, like what two numbers to multiply, is included in the most efficient way.

As elegant and sophisticated as these codes are, they pale in comparison to nature’s genetic code, which determines how a protein is to be constructed. Unlike the binary 0 and 1 system used by computers, the genetic code uses four chemical nucleotides represented by the letters A, T, G, and C. Triplets of these "letters," called codons, are laid down in a DNA sequence that comprises the program or recipe for the chain of amino acids that make up proteins—the building blocks of life. Like the machine code, the genetic code has been carefully crafted in such a way as to contain redundancy and resist corruption. More remarkable is how this genetic code is optimized in several ways (see “The Genetic Code: Simply the Best,” on page 4). As with computers, spies, or even schoolchildren, none of this remarkable information seems possible apart from the work of a very clever designer.



Creation: From, Through, and By the Triune God
Kenneth Richard Samples

A member of my Sunday school class asked me a question after hearing my talk on the Trinity—the biblically derived doctrine of historic Christianity that the one God subsists as three distinct persons: Father, Son, and Holy Spirit.1 He asked: “Which specific person in the Godhead created the world?” I have been asked thousands of questions over the last 20 years of teaching and lecturing in both churches and colleges, but that was the first time anyone ever asked me that particular question. I appreciated the specificity of the query and how it related to the unique Triune nature of God.

According to Scripture, each person within the Godhead was involved in the work of creation. While God the Father was the primary agent in initiating creation, nevertheless God the Son and God the Holy Spirit served as his divine coagents in the creative task. Thus it is proper to say biblically that the Triune God created all things. Consider a brief summary of the scriptural support for each divine person’s involvement in creation.

God the Father as primary agent in creation

In what was likely an early Christian creedal statement (modeled after the Jewish creed, the Shemah in Deuteronomy 6:4), the Apostle Paul identifies God the Father as the ultimate source and initiator of creation. “Yet for us there is but one God, the Father, from whom all things came and for whom we live” (1 Corinthians 8:6a, NIV). The ancient Nicene Creed (one of the important ecumenical creeds of Christendom) notes the Christian church’s acknowledgment of the Father’s primary role in creation by asserting in its first article: “We believe in one God, the Father almighty, maker of heaven and earth, of all things visible and invisible.”2

God the Son as a coagent in creation

In the prologue of the Gospel of John (verses 1-18), the apostle describes the eternal “Word” (later identified as the Incarnate Son) that was with God in the beginning and was also God himself (John 1:1). The Apostle John then identifies God the Son as active in creation alongside the Father: “Through him [the Son] all things were made; without him nothing was made that has been made” (John 1:3, NIV). The Son’s work in creation (see also Colossians 1:16-17; Hebrews 1:2, 10) demonstrates that he possesses the very prerogatives (privileges or rights) of deity. Paul affirms this notion in the second part of 1 Corinthians 8:6: “and there is but one Lord, Jesus Christ, through whom all things came and through whom we live.” With the same descriptive language, Paul attributes to the Son the same powers of creation and providence as the Father (connecting the two divine persons in the creative act).

God the Holy Spirit as a coagent in creation

The second verse of the book of Genesis reveals the Holy Spirit’s active role with the Father in the creation of all things (see also Job 33:4; Psalm 104:30). Moses reveals through divine inspiration that at a very early stage in creation “the Spirit of God was hovering over the waters” (Genesis 1:2, NIV). This act of “hovering” conveys that the third person of the Trinity was nurturing and protecting the newly created order. The Holy Spirit, like the Son, and with the Father, possesses the divine prerogatives. For the Spirit also performs acts that are reserved for God alone.

A sound theological principle in thinking about the Trinity is to recognize that when one member of the Godhead is involved in a work, then in some way all three members are active therein. However, there are clear examples when one member of the Trinity is recognized as the primary agent in performing a given work. For example, as we observed, the Father is the primary agent in creation, whereas the Son plays this role in redemption, and the Holy Spirit in human regeneration (the new birth).

Evangelical theologian Millard Erickson provides a succinct way of thinking about how the three divine persons worked together in creation: “It was the Father who brought the created universe into being. But it was the Spirit and the Son who fashioned it. While the creation is from the Father, it is through the Son and by the Holy Spirit.”3

References:
1. For an exploration of the doctrine of the Trinity, see Kenneth Richard Samples, “How Can God Be Three and One?” in Without a Doubt: Answering the 20 Toughest Faith Questions (Grand Rapids: Baker, 2004), 63-76
2. The Nicene Creed as cited in Ecumenical Creeds and Reformed Confessions (Grand Rapids, CRC publications, 1988), 8.
3. Millard J. Erickson, Introducing Christian Doctrine, ed. L. Arnold Hustad (Grand Rapids: Baker, 1992), 123



EXTRA! EXTRA! READ ALL ABOUT IT!
Jeff Zweerink, Ph.D.

You’re Standing on a Floating Plate

This just in—ice floats in water! Unlike most materials, as liquid water cools to near its freezing point, its density decreases and then expands as it freezes. Thus, colder water and any ice float on the warmer liquid water below.

Seems anticlimactic, doesn’t it? However, if water did not possess this unusual property, Earth’s habitability would dramatically decrease. Ponds, lakes, streams, rivers, and possibly even oceans would freeze completely solid—not just on the surface—more regularly and take far longer to thaw after temperatures rise.

Amazingly, a similar phenomenon occurring deeper in the Earth may be responsible for enabling our planet to maintain the long-standing plate tectonics so critical for enduring life. Recall that Earth consists of a shallow crust, mantle, and an outer and inner core. Moving from the crust toward the core, most of the relevant materials in Earth’s interior absorb water more readily (because both temperature and pressure increase with depth). One material, a mineral called aluminous orthopyroxene found throughout the Earth, exhibits peculiar behavior in the upper mantle (just below the crust) called the asthenosphere. In this region, aluminous orthopyroxene’s capacity to dissolve water drops dramatically, but increases again at greater depths. Therefore, the materials in this region of the mantle absorb less water than those above and below with the consequence that a large abundance of “hydrous” melt exists in the asthenosphere. Think of a cracker sandwich with jelly (as the asthenosphere) in the middle.

Why does all this matter? The melt provides two important functions. First, it significantly weakens the asthenosphere such that it becomes more malleable and fluid. Second, the melt absorbs a tremendous amount of water compared to the other mantle components and, consequently, it dehydrates the region above the asthenosphere called the lithosphere (or crust). The lithosphere is comprised of the crustal plates that migrate over the surface of the Earth. Taken together, these two effects lead to a process—otherwise known as plate tectonics—where the rigid crustal plates “float” on a weakened and malleable asthenosphere.

Another mineral called olivine constitutes the dominant component of Earth’s mantle, and the solubility of water in olivine and orthopyroxene is similar—at least in the absence of aluminum. Until recently, scientists believed that olivine controlled the water storage capacity of Earth’s interior. However, the addition of aluminum increases the solubility of orthopyroxene nearly one hundred times. Consequently, scientists now recognize aluminous orthopyroxene, with its unusual solubility characteristics, as the controlling material responsible for Earth’s ideal tectonic activity.

This discovery also implies constraints on planet sizes where plate tectonics can occur. On planets that are too large (or small), the location of the asthenosphere will be too deep (or shallow) to permit the necessary crustal plate movement. As the authors of the article conclude, the existence of plate tectonics “is possible only in a planet with a water-bearing mantle” (that also contains sufficient aluminum). Such results echo the words of the Creator who fashioned Earth not as “a waste place, but formed it to be inhabited.”

References:
1. Katrin Mierdel et al., “Water Solubility in Aluminous Orthopyroxene and the Origin of Earth’s Asthenosphere,” Science 315 (2007): 364-68.
2. Isaiah 45:18, NASB