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Junk DNA or not?...

bobwtfomg

Critical Thinker
B
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Sep 16, 2012
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It seems the science of genetics is turning into a cat fight over the issue of junk DNA. Last year a big science project called "encode" concluded that large parts of the so called junk DNA wasn't junk after all, now another group of scientists has dismissed their findings and accused them of being not scientists but badly trained technicians. One of them said " When they published their results, it was claimed its conclusions would necessitate the rewriting of textbooks. Well, yes, but only those textbooks about marketing, mass-media hype and public relations.".....Mee ow

http://www.guardian.co.uk/science/2013/feb/24/scientists-attacked-over-junk-dna-claim
 
I don't know, but have they ever tried taking out the "junk" or replacing it with other "junk" and see what happens?
 
Junk DNA is an unfortunate misnomer, similar to "Big Bang". 35 years ago, while an undergraduate, I was taught that by "junk" one meant DNA not directly involved in the translation and transcription into proteins. The term "junk DNA" gives the public the idea that the DNA is junk or useless, just like the term "Big Bang" gives the public the idea there was some sort of explosion.

As for the scientific spat, as usual good science will eventually come to the top. This is the process at work, and we'll just have to wait.
 
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If I'm not mistaken, it's generally believed that much of what we call "junk DNA" may have some regulatory functions, but I've also heard of experiments where mice were bred with their junk DNA spliced out and suffered no ill effects. My uninformed guess is that junk DNA is an evolutionary vestige that could be the result of nucleotide additions or mutated genes for non-essential proteins, and that some of it happened to experience gain-of-function mutations that gave it some regulatory function that would be evolutionarily preserved.
 
General comment: Science is rife with hubristically dismissed notions that later proved important (Copernican theory comes immediately to mind); many often choose to focus only on and discuss the ones that were proved wrong.

Keep an open mind, but just don't let your brain fall out. No one yet fully understands how complete genomes work.

~Dr. Imago
 
I've read the paper that challenges ENCODE's paper, it is open access and can be found at http://gbe.oxfordjournals.org/content/early/2013/02/20/gbe.evt028.full.pdf+html

I think that the most damning argument they put forth is that the definition of functionality used by the ENCODE team is the wrong one. They used the "causal role" definition (in this case specifically they thought it is enough to show a piece of DNA is translated and transcribed), whereas they should have used the "selected effect" (in addition to translation and transcription you have to show that the piece of DNA has undergone selection, that previous copies had the same or a similar function).
 
My guess is that we're going to find a lot of emergent potential uses for a lot of junk DNA while still having a lot of junk DNA that really is just evidence that God colored outside of the lines on accident.
 
The rebuttal paper makes strong points. The ENCODE definition of function is not useful.

An interesting aside though, there are regions called ultra conserved elements. These are 100% identical from mouse to man (so obviously under selection, even more selection than many essential genes). You can delete some of these and observe no phenotype.

http://www.ncbi.nlm.nih.gov/pubmed/17803355
 
If nothing else, it means there's something non critical for cosmic rays to hit.

The Genome Research Division of Soapy Solutions Corporation is working on a DNA Defragmentation program. Beta testing has demonstrated the viability of the project, but things have stalled since the two lead researchers tried it on themselves.
They managed to get rid of over 70% of viral and other "junk" DNA and we hope they will take up where they left off quite soon after they hatch.
 
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