Science Literature

Junk DNA must be the most misleading phrase in the vocabulary of evolutionary biologists. Now that researchers have realised that "non-coding" does not mean "useless", discoveries of functionality are commonplace. The latest contribution concerns mobile genetic elements - transposons. "Large swaths of garbled human DNA once dismissed as junk appear to contain some valuable sections, according to a new study". It has been recognised that many of these elements have an association with genes that are significant for early development. According to one of the researchers, "We used to think they were mostly messing things up. Here is a case where they are actually useful".
Next time you hear someone saying that humans share useless genetic information with chimpanzees, it is worth remembering the comment (in the abstract) that conserved sequences are, by extension, functional sequences. We are likely to share elements because we have similar functional needs, not because the sequences are vestigial. Whilst design inferences do not exclude the concept of degradation, they do help to avoid the pitfall of thinking that non-coding sequences are junk and not worth researching. That has been shown to be an argument from ignorance.

Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
Craig B. Lowe, Gill Bejerano, and David Haussler
Proceedings of the National Academy of Sciences USA, published April 26, 2007, 10.1073/pnas.0611223104

Abstract: At least 5% of the human genome predating the mammalian radiation is thought to have evolved under purifying selection, yet protein-coding and related untranslated exons occupy at most 2% of the genome. Thus, the majority of conserved and, by extension, functional sequence in the human genome seems to be nonexonic. Recent work has highlighted a handful of cases where mobile element insertions have resulted in the introduction of novel conserved nonexonic elements. Here, we present a genome-wide survey of 10,402 constrained nonexonic elements in the human genome that have all been deposited by characterized mobile elements. These repeat instances have been under strong purifying selection since at least the boreoeutherian ancestor (100 Mya). They are most often located in gene deserts and show a strong preference for residing closest to genes involved in development and transcription regulation. In particular, constrained nonexonic elements with clear repetitive origins are located near genes involved in cell adhesion, including all characterized cellular members of the reelin-signaling pathway. Overall, we find that mobile elements have contributed at least 5.5% of all constrained nonexonic elements unique to mammals, suggesting that mobile elements may have played a larger role than previously recognized in shaping and specializing the landscape of gene regulation during mammalian evolution.

See also:

'Junk' DNA Now Looks Like Powerful Regulator, Scientists Find
Science Daily, April 24, 2007