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On the Origin of Codes, Computers, and Clocks


Recent findings have revealed more wonders about the intricate signaling, processing and timekeeping mechanisms in nature. Here are more opportunities to explore Darwinian vs. design explanations.


Researchers tried to "evolve" the genetic code by blind processes, but news item from the University of Illinois at Urbana-Champaign can’t help marveling at the code’s factory-like integration:

The researchers focused on aminoacyl tRNA synthetases, enzymes that "read" the genetic information embedded in transfer RNA molecules and attach the appropriate amino acids to those tRNAs. Once a tRNA is charged with its amino acid, it carries it to the ribosome, a cellular "workbench" on which proteins are assembled, one amino acid at a time.

Synthetases charge the amino acids with high-energy chemical bonds that speed the later formation of new peptide (protein) bonds. Synthetases also have powerful editing capabilities; if the wrong amino acid is added to a tRNA, the enzyme quickly dissolves the bond.

"Synthetases are key interpreters and arbitrators of how nucleic-acid information translates into amino-acid information," said Gustavo Caetano-Anoll�s, a University of Illinois professor of crop sciences and of bioinformatics. … "Their editing capabilities are about 100-fold more rigorous than the proofreading and recognition that occurs in the ribosome. Consequently, synthetases are responsible for establishing the rules of the genetic code." (Emphasis added.)

From there, after describing protein domains as the "gears, springs and motors that work together to keep the protein machinery running," the article degenerates into an evolutionary story that strains credibility, summarized from a paper in PLOS ONE, that assumes Darwinian evolution rather than demonstrating it:

Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness were likely internalized into the emerging genetic system with the early rise of modern protein structure.

Needless to say, this tale of "emergence of codon specificities" and "archaic synthetases" requires heavy doses of imagination.

Meanwhile, at University of California, San Francisco researchers found another characteristic of intelligently designed codes: grammar. They

have probed deep into the cell’s genome, beyond the basic genetic code, to begin learning the "grammar" that helps determine whether or not a gene gets switched on to make the protein it encodes.

This article had nothing to say about evolution. It’s about enhancers that activate genes (formerly considered as "junk DNA").

The researchers determined that key bits of DNA, called "enhancers," which serve as a type of gene regulator, do not operate in an all-or-nothing manner to control whether or not genes are active. Instead, the researchers found that changes in the arrangements of specific DNA sequences within these enhancers result in changes in levels of gene activity, similar to the way changing the syntax of a sentence affects its meaning.


Those who have dabbled in computer programming may be familiar with "pointers." These are placeholders in code that permit information to be put in later. We are familiar with form letters, for instance, that have generic fields for later inclusion of name and address. This "computer-like mechanism" has been found at work in the human brain, the University of Colorado at Boulder announces. The researchers found a comparable mechanism that allows our "pointers" to fill in the variables when we encounter unfamiliar situations.

Our brains give us the remarkable ability to make sense of situations we’ve never encountered before — a familiar person in an unfamiliar place, for example, or a coworker in a different job role — but the mechanism our brains use to accomplish this has been a longstanding mystery of neuroscience.

Now, researchers at the University of Colorado Boulder have demonstrated that our brains could process these new situations by relying on a method similar to the "pointer" system used by computers. "Pointers" are used to tell a computer where to look for information stored elsewhere in the system to replace a variable.

Although the brain and computer pointing mechanisms work differently, the concept is the same. And what a concept! It almost shouts design: a system that presupposes that variables can be filled in by references to other information. Would the system work if the pointing were inaccurate?


If one clock is evidence of design, how about two or three? For decades, scientists have been studying the built-in diurnal clock common to all life that governs many biological activities on a roughly 24-hour scale. Now, they are identifying additional independent timekeeping mechanisms that may be widespread in biology.

Nature News described some of the research into multi-clock phenomena that is shedding light on several biological mysteries: how do some fish and other marine animals know when to spawn by the tides? What controls the menstrual cycle?

Some marine invertebrates have at least two internal clocks, which follow different times and have different mechanisms, according to two new studies. Multiple timepieces might prove common among animals.

The article gives an example: a "bristle worm" furnished with "a biological clock that follows lunar phases, which is ruled by a separate mechanism than the circadian clock that is synchronized with the Sun." Other animals also have this "circalunar" clock to follow the moon, or a "circatidal" clock to follow the tides. These can operate independently of each other and do not always require light. In addition, various animals appear to have separate and distinct mechanisms that operate these clocks. Even we humans may have multiple timepieces. A Swiss researcher says "there is clear evidence of multiple clocks in humans as well."


Codes, computers, clocks — what can we conclude about their origin? William Paley famously used his "watchmaker argument" to argue for design of a storied watch discovered on a heath. Now, we know of real clocks made of biomolecules. Paley knew nothing of computers, and lived before Morse Code was designed.

As leading ID exponents including Dembski, Behe, Wells and Meyer explain, Paley went too far. He was motivated to defend the God of the Bible as the Designer; consequently, he drew inferences that went beyond the evidence. Modern intelligent design theory is different. ID does not try to identify the watchmaker, if there is one. It makes more modest inferences: simply, is there design or not?

ID reasons from the evidence alone to decide among chance, natural law, or design as the best inference. It leaves downstream questions like the identity or character of the designer in the hands of philosophers or theologians. Because of this, ID remains within science, as illustrated in its regular, non-theological uses in diverse scientific fields like archaeology, forensics, and cryptology.

When we see codes, computers and clocks, we intuitively recognize design; but science sets a higher standard than intuition. First, we must consider the explanatory possibilities. If we can argue that design and non-design exhaust the explanatory space, the rule of uniformity is a second check: from our uniform experience, where do these types of multi-part, functional, information-rich systems come from? If we answer design, the design filter must be applied to test the inference. Do these biological mechanisms possess specified information of sufficient complexity to surpass the universal probability bound? If so, then chance and natural law can be rejected, and a design inference is justified. ID can rigorously defend what our intuitions tell us: codes, computers, and clocks are products of mind.

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