Today’s New Reason To Believe

Posted by Fazale ‘Fuz’ Rana, Ph.D.

New Study Uncovers More Evidence for Biochemical Optimization and Intelligent Design

Most people who do a lot of writing find a thesaurus a valuable resource. Having a list of synonyms handy helps writers carefully choose the best word, making their writing more exact. It also helps them avoid using the same word over and over again.

As helpful as a thesaurus might be, it can cause problems if not properly used. Synonyms are not always interchangeable, and if little thought is given to synonym selection, a nonsensical sentence can result.

Synonyms are not exclusive to human languages. They are also part of the biochemical information systems of the cell. (Go here for an article on biochemical information.) “Biochemical synonyms” (also called codons) are an integral part of the genetic code, the set of rules that define the cell’s information systems. The cell’s machinery uses these rules to produce proteins from the information stored in DNA.

In recent years, biochemists have discovered that these biochemical synonyms (codons) are not completely interchangeable, like some synonyms in the English language. (For example, go here for a technical article that illustrates this newly recognized phenomenon.) It turns out that some codons are better suited than others for producing functional proteins. Biochemists refer to these preferred biochemical synonyms as optimal codons.

A new study demonstrates that the usage of such codons appears to be optimized, providing added evidence that life stems from the work of a Creator. This week I will present the background information necessary to appreciate this new insight (or understanding, if you consult a thesaurus). A good place to start is with proteins.

Proteins

This class of biochemicals serves as the “workhorse” molecules of life, taking part in essentially every cellular and extracellular structure and activity. These compounds help form structures inside the cell and in the cell’s surrounding matrix. Among other roles, proteins catalyze chemical reactions, harvest chemical energy, participate in the cell’s defense systems and store and transport molecules.

Proteins are chain-like molecules that fold into precise three-dimensional structures. The protein’s three-dimensional architecture determines the way it interacts with other proteins to form larger complexes. The structure of the folded protein dictates its function.

Proteins form when the cellular machinery links together (in a head-to-tail fashion) smaller subunit molecules called amino acids. The cell employs twenty different amino acids to make proteins. The amino acids that make up the cell’s protein chains possess a variety of chemical and physical properties. In principle, amino acids can link up in any of the possible amino acid combinations and sequences to form a protein.

Each amino acid sequence imparts the protein chain with a unique chemical and physical profile along its chain. As amino acids along the length of the chain attract and repel each other, the chemical and physical profile determines how the protein chain folds. Because structure determines the function of a protein, the amino acid sequence ultimately defines the type of work the protein performs.

Not all the amino acids in a protein chain are equal. Some are critical residues, meaning that if they are replaced by another amino acid, the protein chain will not properly fold and will lose function. Others can be substituted with little consequence to the protein’s structure and function. Biochemists refer to these amino acids as variable.

DNA

Like proteins, DNA consists of chain-like molecules known as polynucleotides. Two polynucleotide chains align in an antiparallel fashion to form a DNA molecule. (The two strands are arranged parallel to one another with the starting point of one strand located next to the ending point of the other strand, and vice versa.) The paired polynucleotide chains twist around each other forming the well-known DNA double helix. The cell’s machinery forms polynucleotide chains by linking together four different subunit molecules called nucleotides. The four nucleotides used to build DNA chains are adenosine, guanosine, cytidine, and thymidine, familiarly known as A, G, C, and T, respectively.

DNA stores the information necessary to make all the proteins used by the cell. The sequence of nucleotides in the DNA strands specifies the sequence of amino acids in protein chains. Scientists refer to the amino-acid-coding nucleotide sequence (for constructing proteins) as a gene. Through the use of genes, DNA stores the information functionally expressed in the amino acid sequences of protein chains.

The Genetic Code

At first glance, there appears to be a mismatch between the storage and functional expression of information in the cell. A one-to-one relationship cannot exist between the four different nucleotides of DNA and the twenty different amino acids used to assemble proteins. The cell overcomes this mismatch by using a code comprised of groupings of three nucleotides, called codons, to specify the twenty different amino acids.

The cell uses a set of rules to relate these nucleotide triplet sequences to the twenty amino acids comprise proteins. Molecular biologists refer to this set of rules as the genetic code. The nucleotide triplets represent the fundamental units of the genetic code. The genetic code uses each combination of nucleotide triplets to signify an amino acid. This code is essentially universal among all living organisms.

Sixty-four codons make up the genetic code. Because the genetic code only needs to encode twenty amino acids, some of the codons are redundant. That is, different codons code for the same amino acid. In fact, up to six different codons specify some amino acids. Other amino acids are specified by only one codon.

As I discussed in my book The Cell’s Design, the rules of the genetic code and the nature of the redundancy appear to be designed to minimize errors in translating information from DNA into proteins that would occur due to substitution mutations. This optimization stands as evidence for the work of an Intelligent Agent.

Mutations

A mutation refers to any change that takes place in the DNA nucleotide sequence. DNA can experience several different types of mutations. Substitution mutations are one common type. When a substitution mutation occurs, one (or more) of the nucleotides in the DNA strand is replaced by another nucleotide. For example, an A may be replaced by a G, or a C may be replaced by a T. This substitution changes the codon that the nucleotide takes part in. Interestingly, the genetic code is structured in such a way so that when substitution mutations take place, the resulting codon specifies the same amino acid (due to redundancy) or an amino acid that has similar chemical and physical properties to the amino acid originally encoded. This cleverly orchestrated relationship further evinces Intelligent Design.

When substitution mutations generate a new codon that specifies the same amino acid as initially encoded, it’s referred to as a synonymous mutation. When a substitution, however, produces a codon that specifies a different amino acid, it’s called a nonsynonymous mutation.

Nonsynonymous mutations can be deleterious if they affect a critical amino acid or if they significantly alter the chemical and physical profile along the protein chain. If the substituted amino acid possesses dramatically different physicochemical properties from the native amino acid, the protein folds improperly. This improper folding impacts the protein, yielding a biomolecule with reduced or even lost function.

Synonymous Mutations are not Interchangeable

Biochemists used to think that synonymous mutations had no impact whatsoever on protein structure, and hence function, since the amino acid sequence specified by the synonymous change would be identical.

Recently, biochemists have recognized that their perception about synonymous changes was wrong. Even though the amino acid sequence hasn’t changed, the protein structure can be altered. One hypothesis involves the speed with which the cell’s machinery reads the information used to direct the production of the protein chain. Some codons are read faster by the cell’s machinery than others. And this reading rate affects the production speed of the protein chain. When proteins are produced they are put together in an assembly line-like fashion, with one amino acid added at a time. As the protein chain is assembled, it starts to fold before it’s built in its entirety. And the folding pattern will change depending upon the pace of the protein’s construction.

Another explanation has to do with the tendency of the cell’s machinery to make mistakes when reading codons. Some codons that are part of a synonymous codon list are more likely to be misread than others. So even though the information needed to make a particular protein hasn’t changed, the wrong amino acid still may be introduced into the protein chain because of the codon used. This error, of course, can lead to structural and functional abnormalities in that protein, just as if a nonsynonymous change had occurred.

This recent insight about the nonequivalency of synonymous mutations set the stage for biochemists to discover that the usage of the optimal codons is, indeed, optimal.

I’ve gone on long enough for now. Or to say it another way, I’ll save the rest of the discussion for next week, when I will describe this research and discuss its implications.

by Dr. Jeffrey Zweerink

My graduate research focused on detecting extremely energetic gamma rays from astronomical objects. Using an arbitrary set of units, if the light from a standard incandescent bulb has the energy of one, then the X-rays in a doctor’s office have energy around 10,000. The gamma rays I searched for had energies 100 million times larger than the doctor’s X- rays. Astronomical objects capable of producing such high-energy radiation must exhibit some of the most extreme environments in the universe.

Detected in 1988, the first discovered high-energy gamma-ray emitting object is the Crab Nebula. In the middle of this nebula resides a star with a mass about 1.5 times the mass of the sun. However, this star is only 15 to 20 miles across and spins around 30 times a second! Objects like this—known as neutron stars—often emit opposing beams of radio emission. If the radio beam(s) pass across Earth as the neutron star rotates, astronomers call them pulsars.

Beyond emitting gamma rays, the large masses and small sizes of neutron stars also generate huge gravitational fields that astronomers use to test the validity of general relativity. One particular object, with the functional but boring name of PSR J0737—3039A/B, consists of two pulsars orbiting one another every 2.45 hours. Additionally, the magnetic field surrounding one of the pulsars (the blue region in the image below) eclipses the radio emission of the other for roughly 30 seconds each orbit.

In the past, this object has provided four independent timing tests of general relativity. As described in a recent Science article (see the article in Science Daily also), an international team of astronomers and physicists took advantage of the eclipsing nature of the binary pulsar PSR J0737-3039A/B to perform a different test. If general relativity accurately describes how gravity operates, the axis around which a pulsar spins should change direction like the gyroscope below (called precession) with a specific rate.

The team was able to determine the precession rate of pulsar A using precision measurements of its pulsations as the magnetic field of pulsar B eclipsed its radio beam. The measured precession matched the value predicted by general relativity. These results provide another confirmation of general relativity in a regime where it most likely would break down—in the presence of strong gravitational fields.

RTB’s creation model assumes that general relativity gives an accurate description of the development of the universe. Consequently, this new test further strengthens the model and gives support to its central premise that the God of the Bible created the universe with humanity in mind.

Kenneth Richard Samples

The laws of physics are discovered by human beings, not invented. But would you say the same about ethical laws? Are ethical principles invented or discovered?

What is good (ethics) cannot exist in a metaphysical (relating to reality) and epistemological (relating to truth) vacuum. One’s view of appropriate human conduct will have a lot to do with what a person thinks about the nature of reality and truth. In other words, one’s ethical views are greatly impacted by one’s broader and more comprehensive worldview.

In the first two articles in this series I provided definitions of key terms used in the formal study of ethics. This article will begin exploring five critical questions that show how a formal system of ethics is impacted by other philosophical considerations.

The Five Problems of Ethics

1. What characterizes human nature?

An adequate worldview should illumine the human condition. A particular worldview’s anthropology (view of humanity) will orient human nature in a specific direction. There are some critical questions that need to be asked about the nature of humanity. Consider the following:

Are human beings born morally good, bad (sinful), or neutral?

It is interesting that the three Middle Eastern monotheistic religions provide three different answers to this important question. Islam strongly asserts that mankind is morally good. Historic Christianity, on the other hand, proclaims that humankind is sinful by nature. Modern-day Judaism insists that human nature is morally neutral. Obviously all three positions cannot be correct.

Another question relates to man’s basic rationality. Judaism and Christianity say that human beings are rational in nature because humans were created in the image of God (Genesis 1:26-27). The Eastern religion of Hinduism, on the other hand, asserts that human beings are unenlightened as to their true nature (man is divine and has forgotten it—a type of cosmic amnesia).

The naturalistic worldview that posits the physical cosmos as the only reality struggles to explain man’s apparent rationality. How can the rational enterprises of logic, math, and science come from a world resulting from a physical accident? And isn’t the mind of human beings also the product of that evolutionary accident?

Identifying human nature is a very important issue in developing a system of ethics.

2. What is the greatest good?

This is where values directly impact ethical considerations. The study of ethics seeks to identify the greatest good (Latin: summum bonum). The philosophical presumption is that life is about identifying the greatest good and appropriately orienting one’s life around it.

But just what is the greatest good? What is the ultimate concern for human beings? What is the goal or object of life itself?

Naturalistic evolutionists insist that life is all about physical survival. Hedonistic philosophers maintain that pleasure is the main goal. Still others contend that gaining power, wealth, and fame is the primary objective. Eastern religion claims that life is about becoming spiritually enlightened and ultimately becoming one with an impersonal deity (pantheism).

The Bible, however, reveals the greatest good as being God himself (an infinite, eternal, and morally perfect being, the Creator of the cosmos, and the Redeemer of lost sinners). A saving relationship with God through the gospel is central to the historic Christian message. The Bible describes salvation as enjoying a loving relationship with God forever (John 3:16).

In ensuing articles I will explore the three other questions that make up “the five problems of ethics.”

For more on the study of ethics, see chapters 16 and 18 of my book Without a Doubt: Answering the 20 Toughest Faith Questions and chapters 1 and 11 of my book A World of Difference: Putting Christian Truth-Claims to the Worldview Test.