Junk DNA


The central dogma of molecular biology, as proposed in 1970 by Francis Crick and James Watson, holds that genetic information is transferred from DNA to functional proteins by way of messenger RNA (mRNA). This suggests that mRNA has but a single role, that being to encode for proteins.

Now, a cancer genetics team at Beth Israel Deaconess Medical Center (BIDMC) suggests there is much more to RNA than meets the eye.

In a study appearing in the June 24, 2010 issue of Nature, the authors describe a new regulatory role for RNA — independent of their protein-coding function – that relies on their ability to communicate with one another. Of potentially even greater significance, because this new function also holds true for thousands of noncoding RNAs, the discovery dramatically increases the known pool of functional genetic information…

“Because this new function does not depend on the blueprint that RNAs harbor in their protein-encoding nucleotide sequence, the discovery additionally holds true for the thousands of noncoding RNA molecules in the cell,” explains senior author Pier Paolo Pandolfi, MD, PhD, Director of Research at the BIDMC Cancer Center and George C. Reisman Professor of Medicine at Harvard Medical School.”This means that not only have we discovered a new language for mRNA, but we have also translated the previously unknown language of up to 17,000 pseudogenes and at least 10,000 long non-coding (lnc) RNAs. Consequently, we now know the function of an estimated 30,000 new entities, offering a novel dimension by which cellular and tumor biology can be regulated, and effectively doubling the size of the functional genome.”…

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May 06, 2010 — It’s sometimes difficult to assess the impact of a scientific paper when it is first published, but one that came out on the cover of Nature today has potential to equal the discovery of the genetic code.  The leading science journal reported the discovery of a second genetic code – the “code within the code” – that has just been cracked by molecular biologists and computer scientists.  Moreover, they used information technology – not evolutionary theory – to figure it out.

The new code is called the Splicing Code.  It lives embedded within the DNA.  It directs the primary genetic code, in very complex but now predictable ways, how and when to assemble genes and regulatory elements.  Cracking this code-within-a-code is helping elucidate several long-standing mysteries about genetics that emerged from the Human Genome Project: Why are there only 20,000 genes for an organism as complex as a human being? (Scientists had expected far more.)  Why are genes broken up into segments (called exons), separated by non-coding elements (called introns), and then spliced together after transcription?  And why are genes turned on in some cells and tissues, but not in others?  For two decades molecular biologists have been trying to figure out the mechanisms of genetic regulation.  This important paper represents a milestone in understanding what goes on.  It doesn’t answer all the questions, but it shows that an inner code exists – a communication system that can be deciphered so clearly, that the scientists could predict what the genome would do in certain situations with uncanny accuracy.

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A good article by Casey Luskin over at Evolution News and Views:

When large-scale function was detected for non-coding DNA (once called “junk” DNA) Darwinists, knowing that their viewpoint had long boasted that junk-DNA was evidence for common ancestry and that they were losing that argument, responded in one of two ways: Some sought to rewrite history by claiming that evolutionary biology predicted all along that we’d find function for junk-DNA. Others, however, pushed the “junk” back to RNA. They effectively argued, “Sure, we know that most of the genome is being transcribed into RNA, but that doesn’t mean that the RNAs have function. Much of the transcriptome might in fact be junk.” Evolutionist biochemist Larry Moran, for example, argued that either “[t]he so-called transcripts are just noise from accidental transcription” or “[t]he regions of junk DNA could be transcribed regularly but the transcripts are rapidly degraded. They do not have a biological function. They are junk RNA.” Intelligent design (ID) proponents were quick to predict the demise of that argument, and if a recent paper in Nature is any indication, “junk RNA” may have the same fate as “junk DNA.”…

The article makes an extremely important point: “Strictly speaking, the absence of evolutionary conservation cannot prove the absence of function.” This is important because in his book, The Language of God, theistic evolutionist Francis Collins argues that a greater level of differences among species’ non-coding DNA than among their protein-coding DNA serves as evidence that the non-coding DNA is “junk.” The alternative, of course, is that the large differences within non-coding DNA serve important functions that may actually help determine the differences between species themselves. In other words, the genetic holy grail — the differences in DNA that determine differences between species — was staring Collins in the face and he dismissed it as genetic junk. This shows how the “junk” DNA paradigm is deeply embedded within Darwinian thinking, and can serve to stifle scientific advance…

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May 10, 2007 (Science Daily) – A tiny opossum’s genome has shed light on how evolution creates new creatures from old, showing that change primarily comes by finding new ways of turning existing genes on and off.

The research, by an international consortium led by the Broad Institute of MIT and Harvard, revises our understanding of genetic evolution. Scientists previously thought that evolution slowly changed the genes that create specific proteins. As the proteins changed, so did the creatures that owned them.

The current research shows that opossum and human protein-coding genes have changed little since their ancestors parted ways, 180 million years ago. It has been the regulation of their genes – when they turn on and off – that has changed dramatically.

“Evolution is tinkering much more with the controls than it is with the genes themselves,” said Broad Institute director Eric Lander. “Almost all of the new innovation … is in the regulatory controls. In fact, marsupial mammals and placental mammals have largely the same set of protein-coding genes. But by contrast, 20 percent of the regulatory instructions in the human genome were invented after we parted ways with the marsupial.”…

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Interestingly, the next part in the series I’ve been writing here deals with issues similar to this. But I should point out a couple of things here, since that post will not deal with this completely:

University of Iowa scientists have made a discovery that broadens understanding of a rapidly developing area of biology known as functional genomics and sheds more light on the mysterious, so-called “junk DNA” that makes up the majority of the human genome.

The team, led by Beverly Davidson, Ph.D., a Roy J. Carver Biomedical Research Chair in Internal Medicine and UI professor of internal medicine, physiology and biophysics, and neurology, have discovered a new mechanism for the expression of microRNAs — short segments of RNA that do not give rise to a protein, but do play a role in regulating protein production. In their study, Davidson and colleagues not only discovered that microRNAs could be expressed in a different way than previously known, they also found that some of the junk DNA is not junk at all, but instead consists of sequences that can generate microRNAs.

“Not so many years ago our understanding was that DNA was transcribed to RNA, which was then translated to protein. Now we know that the levels of control are much more varied and that many RNAs don’t make protein, but instead regulate the expression of proteins,” Davidson explained. “Non-coding RNA like microRNAs represent a set of refined control switches, and understanding how microRNAs work and how they are themselves controlled is likely to be very important in many areas of biology and medicine.”

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The term junk DNA refers to those portions of the genome which appear to have no specific purpose. But a team from IBM has identified patterns, or “motifs”, that were found both in the junk areas of the genome and those which coded for proteins. The presence of the motifs in junk DNA suggests these portions of the genome may have an important functional role. The findings are reported in Proceedings of the National Academy of Sciences journal. But they will have to be verified by experimenters in the lab, the scientists behind the work point out.

Dr Andrew McCallion, who was not an author on the new paper, commented: “Up until not so long ago, we were under the impression that the vast majority of information in the genome, if not all of it, was encoded in those stretches of DNA that encoded proteins.

“We now understand there is much more complexity involved,” Dr McCallion, from the McKusick-Nathans Institute of Genetic Medicine at the Johns Hopkins University School of Medicine in Baltimore, US, told the BBC News website.

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