William Dembski argued in No Free Lunch that intelligent design theory yields no false positives: the Design Filter he modeled doesn’t allow them. False negatives might slip through — things that look random but are in fact designed, like some recent works of art one can think of. But the filter is robust with respect to things that look designed but can be explained by natural law or chance, like snowflakes and tornados.

In this context, ID gains confidence by not finding false positives in the genome, but on the contrary, watching false negatives turn into true positives.

The intelligent-design community might, indeed, be troubled by now if what we thought was genomic design turned out to be junk. On the contrary, this news from Washington University in St. Louis is becoming a familiar refrain:

So-called junk DNA was long thought to have no important role in heredity or disease because it doesn’t code for proteins. But emerging research in recent years has revealed that many of these sections of the genome produce RNA molecules that, despite not being proteins, still have important functions in the body. (Emphasis added.)

Here are some recent findings that say as much.

Long non-coding RNA. "Non-coding" bits of genetic information were assumed to be junk in the past. Not any more: scientists at Case Western Reserve University have found that lncRNAs can, despite their name, code for proteins.

Case Western Reserve School of Medicine scientists have made an extraordinary double discovery. First, they have identified thousands of novel long non-coding ribonucleic acid (lncRNA) transcripts. Second, they have learned that some of them defy conventional wisdom regarding lncRNA transcripts, because they actually do direct the synthesis of proteins in cells.

This suggests that even more function awaits discovery. The findings were made in yeast, but probably hold for higher animals and humans: "Discovery of more transcripts equates to the discovery of new and novel genes:"

Information in the geometry. There’s information in the "wobble" of a machine that grafts amino acids onto transfer RNAs, as news from Japan’s RIKEN says. Note all the intelligent-design language:

When proteins are produced in cells based on the "genetic code" of codons, there is a precise process under which molecules called transfer RNA (tRNA) bind to specific amino acids and then transport them to cellular factories called ribosomes where the amino acids are placed together, step by step, to form a protein. Mistakes in this process, which is mediated by enzymes called synthetases, can be disastrous, as they can lead to improperly formed proteins. Thankfully, the tRNA molecules are matched to the proper amino acids with great precision, but we still lack a fundamental understanding of how this selection takes place.

By studying one of the synthetases that matches alanine to its proper tRNA, they found that its amazing specificity is partly due to the way it "wobbles" to ensure that alanine, and not a look-alike, gets fastened (see the news report in Nature). A single base-pair mutation, they found, reduces binding by a hundredfold. This implies that there is "a specific recognition signal" in the wobble itself.

Still, one of the researchers found a way to insert the word "evolution" into a discovery that has design all over it like white on rice:

According to Yokoyama, "this is a fascinating finding that may give us new insights into how living systems can so accurately translate their genetic code through processes that are at their core stochastic or random, using even small structural changes. Our work is interesting in terms of the evolution of the genetic code, since acceptor stem recognition is important for the concept of the ‘second genetic code’. The findings in this paper may show a previously unknown mechanism of tRNA recognition inherited from a distant ancestor."

No such "distant ancestor" is, however, identified.

Rise of the epigenome. Early geneticists following Watson and Crick did not expect to find information beyond the A, T, C, and G letters they identified as the genetic code. Now, hidden storehouses of additional information are opening up to view, becoming more vital, in some cases, than the genes themselves.

Puzzled by the lower-than-expected count of actual protein-coding genes in the human genome, researchers at CNIO (Centro Nacional de Investigaciones Oncologicas) in Spain started thinking that they needed to look outside the genome for the extra information — especially after Alfonso Valencia’s team revised downward the number of human genes to 19,000.

"The shrinking human genome," that’s how Valencia describes the continuous corrections to the numbers of the protein-coding genes in the human genome over the years that has culminated in the approximately 19,000 human genes described in the present work. "The coding part of the genome [which produces proteins] is constantly moving," he adds: "No one could have imagined a few years ago that such a small number of genes could make something so complex."

Even more puzzled that so few genes separate humans from other primates, or from mice, or even from the one-millimeter sized lab roundworm Caenorhabditis elegans, they figured that the genome cannot be the whole story. There must be a way that the genome is "doing more with less." The article explains, "The physiological and developmental differences between primates are likely to be caused by gene regulation rather than by differences in the basic functions of the proteins in question." But where would the regulatory information be stored?

The sources of human complexity lie more in how genes are used rather than on the number of genes, in the thousands of chemical changes that occur in proteins or in the control of the production of these proteins by non-coding regions of the genome, which comprise 90% of the entire genome and which have been described in the latest findings of the international ENCODE project, a Project in which the Valencia team participates.

In short, there is more information in the genomes of organisms than first appears by counting genes. Attachment of methylation tags (the "histone code") is one such mechanism that has been studied for years now. A recent paper in PNAS identified an "evolutionarily conserved" epigenetic marker in rice that, if mutated, causes death of the plant. Genome stability in both animals and plants depends on the molecular machine that attaches this tag correctly, the paper says.

Ribosomal frameshifting: Shifting the triplet code by a single letter might seem like a recipe for disaster, but scientists at the University of Maryland found a method in the madness. "Frameshifting," in which codons in the ribosome are read from the second letter instead of the first, provides an "alternate operating manual," they say. Cells use the shift to good advantage in certain situations.

Working with a gene that plays a critical role in HIV infection, University of Maryland researchers have discovered that some human genes have an alternate set of operating instructions written into their protein-making machinery. The alternate instructions can quickly alter the proteins’ contents, functions and ability to survive.

Their term "programmed ribosomal frameshifting" is suggestive of function. The UM scientists’ paper in Nature "is the first to show that a human gene uses programmed ribosomal frameshifting to change how it assembles proteins." During a disease attack, for instance, a gene might want to frameshift its code so that a nonsense RNA transcript results, yielding a polypeptide that would be destroyed after exiting the ribosome. Why would that be good? Maryland’s Jonathan Dinman thinks it could act like "a dimmer switch, lowering the immune response to a safe level," thus avoiding excessive inflammation.

"Dinman has long suspected that human cells also have frameshift signals, and that they are useful," we learn. That’s science looking for design, not junk.

Image source: Tom Chang/Flickr.