If the essence of life is information, as William Dembski argues in his recent book, Being as Communion, we should expect to see signs of intelligent planning in the processes of life at every level. Darwinians, on the other hand, expect to see sloppy, clunky mechanisms that just get by. Which view fits the evidence best?

Let’s be honest; every origin story has problems. There are things in nature that challenge intelligent design, just as there are things that defy a Darwinian view of life. One way to bet on the winner is to watch the track record over time. Which view is getting stronger with new evidence? Which view has fewer anomalies to explain as observations accumulate?

Degenerate Coding

Darwinians seemed to have an upper hand decades ago when the genetic code was first elucidated. Why do multiple codons code for the same amino acid in some cases and not others? There are six codons for arginine, for instance, but only one for methionine. Some have two, three, or four matching codons. The genetic code is called "degenerate" for this reason; there isn’t a one-for-one match. Francis Crick called it a "frozen accident" because it didn’t seem to make sense to have so much redundancy.

Now researchers at Case Reserve Western University have offered an explanation for this degeneracy. There’s a method in the madness: the codons work at different speeds, acting like "speed limits" for transcription. The headline reveals they weren’t looking for this when they found it: "Case Western Reserve Scientists Discover Hidden Meaning and ‘Speed Limits’ within the Genetic Code." (Emphasis added.) Lead author Jeff Coller says, "Our discovery is that the genetic code is more complex than we knew."

Things are not looking good for the blind watchmaker. Here’s the upshot:

The most significant breakthrough in the Case Western Reserve work is that all of the words, or codons, in the genetic code are deciphered at different rates; some are deciphered rapidly while others are deciphered slowly. The speed of how mRNA decodes its information is the sum of all the codons it contains. This imposed speed limit then ultimately affects the amount of protein produced. Sometimes faster is better to express a high level of protein. Sometimes slower is better to limit the amount protein. Importantly, codons are redundant — many of these words mean the same thing.

Coller and colleagues found that each of the codons is recognized differently by a ribosome. Some codons are recognized faster than others, but these differences in speed are tiny. Over the entire span of an mRNA, however, each tiny difference in speed is powerfully additive.

The redundancy has a function, therefore. The messenger RNA — depending on how it’s scripted — can fine-tune the amount of protein produced.

Another feature of this built-in speed regulation is that it affects the half-life of the mRNA. This explains what Case Western researchers were looking for: why some transcripts last longer than others. They found that "mRNA translation and mRNA decay are intimately connected." It’s as if speed limits are built into the genetic code; it tells the translation machinery how much to produce, and how fast.

This means that synonymous codons are not strictly redundant or interchangeable. Thinking about this, the scientists realized that the speed limits give medical researchers a new way to adjust transcription rates for their own intelligent designs.

His discovery has a variety of practical implications for medicine. From a bioengineering perspective, molecular biology techniques can be applied to manipulate the gene to contain ideal codons and obtain the gene expression pattern that is most beneficial to the application. From a human physiological standpoint, it’s possible to learn the speed limit for each and every mRNA and then determine if this changes in specific pathologies such as cancer….

"The sky is the limit," Coller said. "Since this finding is so new, we have no idea what the potential is. The next step is to determine if changes in decoding speed can be an underlying mechanism that alters gene expression in human disease."

Would the Darwinian "blind watchmaker" metaphor get scientists this excited? Would it lead to further research? Would it lead to applications toward better medical treatments? Functionality in the redundant code was a prediction of intelligent design, Casey Luskin said last fall.

Karma Hits Dogma

It’s only right that a dogma gets put out of its misery, particularly a Central Dogma like "DNA makes RNA makes protein," as Francis Crick famously expressed it. A news item from Elsevier hammers another nail in the coffin of the Central Dogma. "Going Beyond the Central Dogma of Molecular Biology," it announces; "Rather than Being a One-Way Street, DNA-Directed RNA Transcription May Have Profound Adaptability." The short article explains a "conceptually novel relationship between the genotype (DNA) and the phenotype (the products of the transcription of DNA)." Would you believe — it’s a two-way street? How about an automated defense mechanism against errors?

The method the authors used to make this discovery is termed Single-Cell Transcriptogenomics (SCTG). It allows DNA and RNA sequencing to be performed concurrently on the same single cells taken from a cell population treated with the powerful mutagen ethylnitrosourea. This method allowed the authors, for the first time, to prove the tendency of the transcriptional machinery in the cell to avoid transcribing DNA strands harboring a newly induced mutation. This is likely to be a novel cellular defense mechanism to prevent genetic mutations from being expressed.

It sounds like a defense against neo-Darwinism as well. How can Darwinian evolution proceed when the cell has an automated mechanism to squelch the mutations that it relies on for innovations?

Scrambling Darwin’s Tree

Another item spells trouble for Darwinian dogma. There’s a lot more horizontal gene transfer (HGT) in the human genome than expected, says BioMed Central.

Many animals, including humans, acquired essential ‘foreign’ genes from microorganisms co-habiting their environment in ancient times, according to research published in the open access journal Genome Biology. The study challenges conventional views that animal evolution relies solely on genes passed down through ancestral lines, suggesting that, at least in some lineages, the process is still ongoing.

There goes the reliability of tracing "Darwin’s tree of life" with genetic comparisons. If you didn’t get your genome via common ancestry, all bets are off. Or is that just our opinion?

Lead author Alastair Crisp from the University of Cambridge, UK, said: "This is the first study to show how widely horizontal gene transfer (HGT) occurs in animals, including humans, giving rise to tens or hundreds of active ‘foreign’ genes. Surprisingly, far from being a rare occurrence, it appears that HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing, meaning that we may need to re-evaluate how we think about evolution."

If you would like some new ways to think about evolution, we will be happy to offer some suggestions.

The title of Dembski’s book is Being as Communion. Communion is about sharing. Communication of information has senders and receivers. These don’t have to be sentient agents with minds and free will. Information can be shared between robots and processes. We should not be surprised to find a wealth of information being shared between members of a highly interconnected biosphere that shares a genetic code.

In Dembski’s analysis, the world is a hierarchically designed, cooperative system from the top down. These findings add to the trend in favor of that view, and against the mindless materialist view.