junk DNA

The December 17, 2010 issue of Science has yet another article explaining why the concept of “junk”-DNA should no longer be given much credence: It used to seem so straightforward. DNA told the body how to build proteins. The instructions came in chapters called genes. Strands of DNA’s chemical cousin RNA served as molecular messengers, carrying orders to the cells’ protein factories and translating them into action. Between the genes lay long stretches of “junk DNA,” incoherent, useless, and inert. That was then. In fact, gene regulation has turned out to be a surprisingly complex process governed by various types of regulatory DNA, which may lie deep in the wilderness of supposed “junk.” Far from being humble messengers, RNAs of Read More ›

I was recently asked by an evolutionary biologist where ID can help science generate “new knowledge.” It’s important to realize that when dealing with historical sciences like neo-Darwinian evolution or intelligent design, new knowledge takes the form of both practical insights into the workings of biology in the present day (which can lead to insights into fighting disease), as well as taking the form of new knowledge about biological history and the origin of natural structures. In this regard, I could not disagree more with suggestions that ID closes off inquiry and does not lead to new scientific knowledge. Below are about a dozen or so examples of areas where ID is helping science to generate new knowledge. Each example Read More ›

Scientific American recently reported on what has transpired since the completion of the Human Genome Project ten years ago. When the HGP was first announced in 2000, many scientists said that it would be the key to understanding disease and for developing cures. Ten years later, however, this has not been the case. The human genome project has aided in developing better research and technology, particularly in our abilities to sequence genes. It has also shown us that much of what we once considered junk DNA isn’t really junk at all. (See here, here, here, and here for past ENV discussions on junk DNA). However, scientists are coming to a sobering conclusion that perhaps their models and assumptions on the nature of disease may be mistaken.

Francis Collins is one of the world’s most prominent theistic evolutionists, and now a prominent piece of President Obama’s government. In this clip, God and Evolution contributors and other scholars respond to Francis Collins’ defense of theistic evolution in his book The Language of God. Display content from www.discovery.org Click here to display content from www.discovery.org. Always display content from www.discovery.org Open content directly In his book The Language of God: A Scientist Presents Evidence for Belief (2006) and other writings and interviews, Collins has described the paths that led him from atheism to religious belief and from an impatience with “messy” biology and a preference for the pristine realms of physics and chemistry to a fascination with DNA, RNA, Read More ›

Proponents of intelligent design (ID) have long predicted that many of the features of living systems which are said to exhibit “sub-optimal” design will, in time, turn out to have a rationally engineered purpose. This is one of several areas where ID actively encourages a fruitful research agenda, in a manner in which neo-Darwinian evolution does not. One such area, and a field for which I have long held an inquisitive fascination for, is the subject of so-called “junk DNA,” and the non-coding stetches of RNA which are transcribed from them.

Skepticism of the “junk DNA” paradigm is not a phenomenon which is limited to proponents of ID. This popular view of the genome — while still resonating as the conventional view among neo-Darwinian thinkers — has also been challenged by John Mattick of the University of Queensland and Jim Shapiro of the University of Chicago.

Earlier this month, an article appeared in the journal Cell by a Spanish team. The article announced the discovery of the ability of long non-coding RNA, which are often encoded in DNA near genes known to be important to both stem cells and cancer, to serve as enhancer elements (which promote gene expression).

According to the paper’s Abstract:

A new paper in Nature magazine again shows that what was “once dismissed as junk” turns out to be another astounding example of complex and specified information in the genome and a crucial part of gene regulation. In 2008 Scientific American noted that microRNAs were “once dismissed as junk” and said the following: Tiny snippets of the genome known as microRNA were long thought to be genomic refuse because they were transcribed from so-called “junk DNA,” sections of the genome that do not carry information for making proteins responsible for various cellular functions. Evidence has been building since 1993, however, that microRNA is anything but genetic bric-a-brac. Quite the contrary, scientists say that it actually plays a crucial role in Read More ›

On August 19, Gina Kolata reported in The New York Times that geneticists “have seen a dead gene come back to life and cause a disease.” According to Kolata, the human genome “is riddled with dead genes, fossils of a sort, dating back hundreds of thousands of years–the genome’s equivalent of an attic full of broken and useless junk,” though some of those genes “can rise from the dead like zombies.” Now a supposed “zombie gene” is implicated in a type of muscular dystrophy abbreviated FSHD–a hereditary disease that affects about 1 in every 20,000 people. Kolata cites a recent Science article that begins by reviewing work dating back to the 1990s that establishes a link between FSHD and a Read More ›

Advocates of intelligent design have long been skeptical of the claim that the majority of our genome is nonfunctional gibberish, a mere relic of our evolutionary past. Many of the key arguments for common ancestry are based around the supposition that certain loci of our genome are functionless. But the gaps in our knowledge of the genome (in which such supposition resides) are continually shrinking.

A recent paper published in Science by Kondo et al. reported on the discovery that some of the supposed “non-coding” regions of the RNA transcript actually actively encode for short peptides that regulate genes involved in Drosophila development.

According to the Abstract,

A substantial proportion of eukaryotic transcripts are considered to be noncoding RNAs because they contain only short open reading frames (sORFs). Recent findings suggest, however, that some sORFs encode small bioactive peptides. Here, we show that peptides of 11 to 32 amino acids encoded by the polished rice (pri) sORF gene control epidermal differentiation in Drosophila by modifying the transcription factor Shavenbaby (Svb). Pri peptides trigger the amino-terminal truncation of the Svb protein, which converts Svb from a repressor to an activator. Our results demonstrate that during Drosophila embryogenesis, Pri sORF peptides provide a strict temporal control to the transcriptional program of epidermal morphogenesis.

The literature continues to flood in demonstrating that so-called ‘junk’ regions of the genome are not junk after all, but serve significant and important functions. One such recent paper reports evidence that retrotransposons may play significant roles in the cell. According to the abstract,

Retrotransposons including endogenous retroviruses and their solitary long terminal repeats (LTRs) compose >40% of the human genome. Many of them are located in intergenic regions far from genes. Whether these intergenic retrotransposons serve beneficial host functions is not known. Here we show that an LTR retrotransposon of ERV-9 human endogenous retrovirus located 40–70 kb upstream of the human fetal γ- and adult β-globin genes serves a long-range, host function. The ERV-9 LTR contains multiple CCAAT and GATA motifs and competitively recruits a high concentration of NF-Y and GATA-2 present in low abundance in adult erythroid cells to assemble an LTR/RNA polymerase II complex. The LTR complex transcribes intergenic RNAs unidirectionally through the intervening DNA to loop with and modulate transcription factor occupancies at the far downstream globin promoters, thereby modulating globin gene switching by a competitive mechanism.

Retrotransposons include the long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), endogenous retroviruses (ERVs), and the solitary long terminal repeats (LTRs) of ERVs, and compose over 40% of the human genome. Retrotransposons possess enhancers and promoters which promote the expression of downstream polycistronic gene sequences. The cited paper seeks to determine whether the retrotransposons which are located in the intergenic (regions which intersperse genes, also known as ‘introns’) of the genome – which are often several hundred kilobases removed from the promoters – serve any beneficial function.

A few weeks ago, PZ Myers commented on so-called ‘Junk DNA’. Under the headline, ‘Junk DNA is still junk’, Myers wrote:

The ENCODE project made a big splash a couple of years ago — it is a huge project to not only ask what the sequence of a strand of human DNA was, but to analyzed and annotate and try to figure out what it was doing. One of the very surprising results was that in the sections of DNA analyzed, almost all of the DNA was transcribed into RNA, which sent the creationists and the popular press into unwarranted flutters of excitement that maybe all that junk DNA wasn’t junk at all, if enzymes were busy copying it into RNA. This was an erroneous assumption; as John Timmer pointed out, the genome is a noisy place, and coupled with the observations that the transcripts were not evolutionarily conserved, it suggested that these were non-functional transcripts.