Intelligent Design: The Right Conclusion, but the Wrong Reasons

It is possible to do the right thing, but for all the wrong reasons. In the realm of apologetics, it’s also possible to rightly conclude that life stems from a Creator, but to offer the wrong rationale for this conclusion. From my perspective, this often happens when Christian apologists use molecular information content to make the case for the Creator.

The information content of biomolecules such as DNA and proteins supports one of the most compelling arguments for intelligent design. Often times, Christian apologists emphasize the seemingly vast amount of information housed in a single gene (or protein) and the astronomical improbabilities for that amount of information to ever arise through evolutionary processes. Consequently, they conclude that bio-information and life must originate from a Creator. (I, too, have made a similar argument. See Origins of Life, a book I coauthored with Hugh Ross.)

In my experience, this argument plays well to a lay audience, but has little impact on origin-of-life researchers and biochemists. Their failure to be impressed often prompts many Christians to deride these scientists.

I have wondered for several years: Why the resistance? After spending some time carefully evaluating origin-of-life models and thinking through the matter, I reached an epiphany. The reason why origin-of-life researchers and biochemists are not moved by the information argument has nothing to do with their intransigence. Rather, they resist the argument because it misrepresents the processes that evolutionary biologists credit with generating information-rich molecules, as new research by scientists from Spain illustrates.1

DNA and Proteins: Information-Rich Molecules

Proteins and DNA, both chain-like molecules, form when the cell’s machinery links smaller subunit molecules together, in a head-to-tail manner. Amino acids make up proteins, and nucleotides make up DNA.

In both cases, the molecule’s backbone consists of a repeating structure. Though the backbone is structurally monotonous, the chemical groups that extend from the backbone–the side-chains–differ. The side-chain sequence provides the chemical variability necessary for proteins and DNA to form the numerous chemical structures the cell requires for its activities.

The side-chain sequence variability of proteins and DNA is analogous to the sequences of letters that form words. Just as different letter combinations form a variety of words, different side-chain sequences yield different molecular architectures. Side-chain sequences are a form of information–chemical information–and this makes both proteins and DNA information-rich molecules.

Overlooking Chemical Selection

Can natural processes create the information harbored in proteins and DNA? Many times this question forms the centerpiece of Christian apologists’ argument for intelligent design. Invariably, believers portray it as a probability problem. For example, what is the likelihood that the proteins needed to carry out essential life functions could form through random assembly of amino acids?

This is where Christian apologists make their first mistake. Evolutionary biologists do not think that information-rich molecules originated by random assembly of the subunit molecules into functional biomolecules (which would be properly modeled as a probability problem). Instead, they argue that chemical selection is at work. Chemical selection is a collection of complex processes that are believed to have operated during the origin of life on early Earth. Scientists studying life’s genesis view these processes as nonrandom, meaning that treating the origin of information-rich molecules as a probability problem proves fundamentally inaccurate.

In the lab, origin-of-life researchers have observed the effects of chemical selection throughout the assembly of proteins and RNA molecules from their building block constituents. It is not clear, however, if these selection effects are adequate enough to yield the full breadth of necessary bio-information molecules. This is still an outstanding question in origin-of-life research.

Overlooking the Complexity of Protein Structure-Function Relationships

But even if the assembly of information-rich molecules could be treated as a probability problem, Christian apologists typically fail to properly account for key structural considerations of proteins.

To illustrate my concern, consider the structure of proteins; the cell employs 20 different genetically-encoded amino acids to make these biomolecules. These amino acids possess a range of chemical and physical properties. In principle, the 20 amino acids can link up in any of the possible sequence combinations.

Each amino acid sequence gives the protein chain a specific chemical and physical profile along its length. The amino acids in a protein chain interact with one another in three-dimensional space. Some amino acids attract and others repel. Because of these interactions, the amino acid sequence and the overall chemical and physical properties along the chain cause the protein to fold into a complex and precise three-dimensional structure. The protein’s three-dimensional architecture determines the function it assumes in the cell. To say it another way, the protein’s amino acid sequence determines its structure, and hence, function.

Not all amino acid sequences are equal. Some form proteins with useful functions. Others produce proteins that are “junk” to the cell. These “junk” proteins adopt three-dimensional shapes that have no biochemical utility. The question then becomes: When treated as a probability problem, what is the likelihood that the proteins needed to carry out essential life functions could form through random assembly of amino acids?

In their book, The Mystery of Life’s Origin, chemists Charles Thaxton, Walter Bradley, and Roger Olsen argue that, in the absence of any chemical competition with non-amino acids and non-biologically relevant amino acids, the probability of getting the right amino acid in a specific position in a protein molecule is 1.25 percent. (There is a 50 percent chance of natural processes randomly selecting a left-handed amino acid; a 50 percent chance of joining the two amino acids in the appropriate chemical bond; and roughly a 5 percent chance of selecting the right amino acid.) The probability of undirected processes assembling a protein 100 amino acids in length, therefore, becomes roughly 10-191 (one chance in 10191). Proteins in the cell are typically several hundred amino acids length.

In effect, there is no chance that even a relatively small protein made up of a specified sequence could ever form by undirected processes. In the words of Bradley and Thaxton:

If we assume that all carbon on earth exists in the form of amino acids and that the amino acids are allowed to chemically react at the maximum possible rate of 1012/s for one billion years (the greatest possible time between the cooling of the earth and the appearance of life), we must still conclude that it is incredibly improbable (~10-65) that even one functional protein would be made.2

Wow! This seems like a sufficiently compelling argument—but it has one chief failing. It doesn’t take into account the functional equivalency of amino acids in the protein’s structure.

Functional Equivalency

These types of analyses neglect an important factor that bears on the origin-of-life question, namely that some proteins with different amino acid sequences actually share the same structure and activity. This similarity stems from the fact that some amino acid positions in a protein can be freely varied with no effect on the protein’s structure and function, others can be varied to a limited extent, and some cannot be varied at all. This means that a number of amino acid sequences are biologically indistinguishable from each other. Biochemists refer to this phenomenon as functional equivalency. When functional equivalency is accounted for, the analysis asks, what is the probability that a protein of a specific function (not sequence) would have emerged through undirected processes?

Biochemists are not able to properly determine the probability that a specific protein function will emerge by random chemical events. They simply lack a full understanding of the relationship among amino acid sequence, protein structure, and protein function. In the absence of full knowledge, biophysicist Hubert Yockey estimated this probability for the protein cytochrome C.3

Cytochrome C, which is involved in energy-harvesting pathways, contains about 110 amino acids and is found throughout the living realm. Biochemists have determined the cytochrome C amino acid sequence for numerous organisms. Yockey used this sequence data to estimate the range of variability for each amino acid position in this protein by aligning and comparing all known cytochrome C sequences.

With some understanding of functional equivalency in hand, Yockey determined that the probability of random chemical events stumbling upon a functionally equivalent cytochrome C to be on the order of 10-75. According to Yockey, if one assumes a chemically pristine primordial soup composed of 1044 amino acids, it would take 1023 years at one chance per second to produce a functional cytochrome C. The universe’s age is 14 billion years, less than one-trillionth of the time needed to produce a functional cytochrome C.

Impressive! But again, as compelling as this analysis seems, Yockey’s work suffers one limitation. He may not have identified all possible cytochrome C amino acid sequences. It may be that sequences not known to exist in nature for cytochrome C could yield functional cytochrome C-like proteins. In other words, Yockey’s analysis may not have fully sampled all “sequence space” for functional cytochrome C molecules.

Sequence Space

Based on a computational study, scientists from Spain indicate that protein sequence space may be much more fully occupied than previously thought by Yockey or anyone else.

Protein space refers to all possible amino acid sequence combinations that conceivably exist. Of all those sequences, some are functional, others are not. Sequence space is analogous to the ocean, and the functional sequences within it, to islands. The big question then becomes: How many “islands” are in sequence space and what is the separation among them?

Biochemists (and Christian apologists) have long thought the functional islands population was sparse because proteins are intolerant to changes in amino acid composition (substitutions cause loss in function). In other words, not only was sequence space assumed to be lightly populated, the islands also appeared to feature steep cliffs.

However, the new work from the Spanish scientists indicates that while the islands do possess steep cliffs, the ocean is richly populated with functional regions. The researchers show that while at any point in time 98 percent of amino acid positions cannot be substituted, eventually greater than 90 percent of the amino acid residues in a protein can be altered. This paradox finds explanation in the fact that once one amino acid in the protein is changed it allows invariant positions to change and freely-altered positions to become invariant.

Instead of an ocean populated with a few islands, the researchers believe that protein space is occupied by a “wide-mesh net spanning a large part of sequence space.”4

If these results stand up, it means the likelihood of evolution randomly building functional, information-rich molecules may not be that unthinkable. In this case, the use of probabilities to argue against the evolutionary explanation for the origin of life becomes inadvisable. This is the reason why scientists are unmoved by the probabilities Christian apologists throw around.

But this doesn’t mean that the information argument for intelligent design is totally defunct. The argument just needs to be framed in a different way.

Right Conclusions and Right Reasons

As discussed in my book The Cell’s Design, the best way to use biochemical information to make the case for intelligent design rests on analogical reasoning in the tradition of Watchmaker analogy.

Analogical comparison is an integral part of day-to-day decision-making, but it isn’t neat and tidy. Its conclusions are probabilistic, but not certain. Still, if properly employed, analogical thinking can produce sound conclusions.

The idea behind analogical arguments is this: the structure and function of biochemical systems bear a startling resemblance to the structure and operation of man-made systems. With respect to information systems in the cell:

  • Biochemical Information Systems: Information comes from intelligence. At its essence, the cell’s biochemical systems are information-based. The presence of information in the cell, therefore, must emanate from an intelligent Designer.
  • Structure of Biochemical Information: The evidence for intelligent design goes beyond the mere existence of information-based biochemical systems. Biochemical information displays provocative structural features like language structure and the organization and regulation of genes. These also point to the work of a Creator.
  • Biochemical Codes: These systems employ encoded information such as the genetic code, histone code, and the even parity code of DNA. This type of information requires an intelligent Agent to design the code.
  • Genetic Code Fine-Tuning: The rules that comprise the genetic code are better designed than any conceivable alternative code to resist errors that occur as the genetic code translates stored information into functional information. This fine-tuning strongly indicates that a superior Intelligence designed the genetic code.

(For details, see The Cell’s Design or these articles I wrote, here and here.)

The similarities between man-made information systems and those found in the cell, expressed in the form of an analogy, logically and reasonably leads to the conclusion that biochemical design is intelligent design. Based on this line of reasoning, life does indeed appear to be the work of a Creator.

The right conclusion for the right reasons.


1. Inna S. Povolotskaya and Fyodor A. Kondrashov, “Sequence Space and the Ongoing Expansion of the Protein Universe,” Nature 465 (2010): 922–26.

2. Walter L. Bradley and Charles B. Thaxton, “Information and the Origin of Life” in The Creation Hypothesis: Scientific Evidence for an Intelligent Designer, J. P. Moreland, ed. (Downers Grove, IL: InterVarsity Press, 1994): 190.

3. Hubert P. Yockey, Information Theory and Molecular Biology (Cambridge, UK: Cambridge University Press, 1992), 246–57.

4. Inna S. Povolotskaya and Fyodor A. Kondrashov, “Sequence Space and the Ongoing Expansion of the Protein Universe,” Nature 465 (2010): 922–26.


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