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Posted by on May 13, 2013 in Uncategorized | 10 comments

Another Nail in the Junk DNA coffin

A couple months ago I wrote about Junk DNA and intelligent design. Here’s what I said:

“The Intelligent Design community has been bragging about a supposedly true prediction they made: that ‘junk DNA’ would turn out to have a function. If you recall, ‘junk DNA’ or non-coding DNA, is DNA that does not code for proteins, and some it of it (but not all of it) is thought to be leftovers of evolutionary history. Now it turns out that at least some noncoding DNA does have a function (which isn’t surprising, evolutionary biologists themselves have been saying that for years). To see the Intelligent Design myth busted, I’d suggest PZ Myers’ Skepticon talk here and a new scientific paper published here.”

Now we can do even better than that. Here’s some new research on the issue:

“[A] new study offers an unexpected insight: The large majority of noncoding DNA, which is abundant in many living things, may not actually be needed for complex life, according to research set to appear in the journal Nature.

“The clues lie in the genome of the carnivorous bladderwort plant, Utricularia gibba.

“The U. gibba genome is the smallest ever to be sequenced from a complex, multicellular plant. The researchers who sequenced it say that 97 percent of the genome consists of genes — bits of DNA that code for proteins — and small pieces of DNA that control those genes.

“It appears that the plant has been busy deleting noncoding ‘junk’ DNA from its genetic material over many generations, the scientists say. This may explain the difference between bladderworts and junk-heavy species like corn and tobacco — and humans.”

Read more from Sciencedaily.

  • qbsmd

    I wish the article had given the researcher’s speculations on why this species had a selective pressure toward getting rid of non-coding DNA. I suspect there are some selective pressures toward having junk DNA and some selective pressures toward not having it, and these pressures balance at different levels for different organisms. For example, birds are selected to be lighter which translates toward less DNA than mammals, while in some plants, like onions, there is effectively no selective pressure against having lots of non-coding DNA and as a result end up with random amounts.

    • ncovington89

      “birds are selected to be lighter which translates toward less DNA than mammals” what evidence supports this statement?

    • GeorgeLocke

      Note if there were selective pressure to get rid of non-coding DNA if non-coding DNA, that would imply that ncDNA has some phenotypic effect: no phenotype means nothing for selection to act on.

      • qbsmd

        There are phenotypic effects. Having more DNA than an organism needs means that it needs to make or digest more nucleic acids before replicating, and either takes longer to copy its DNA or needs more enzymes to copy its DNA. It also results in larger nucleii and larger cells.

        Maybe for some organisms that difference doesn’t matter. Plants already have organelles that basically just take up space, so cell size probably isn’t strongly effected by some extra DNA. For organisms with cells that don’t divide rapidly, the extra DNA wouldn’t matter as much either.

        For other organisms, there is clearly a selective pressure to get rid of it, and clearly organisms can survive without it or with much less of it. I would speculate that for related groups of organisms with very similar genome sizes there are costs and benefits that balance for a certain amount of junk DNA.

        • GeorgeLocke

          good point. even if it is “pure junk”, it has to be replicated, etc, and it has an effect. Plus, even junk DNA seems to get transcribed, which must have some cost.

  • Reginald Selkirk

    Biochemist and textbook author Larry Moran has commented extensively about junk DNA at his blog Sandwalk.

  • CollegeDropoutGuy

    An alternate perspective is found in The Selfish Gene, basically, that ‘junk’ DNA doesn’t need a purpose. We’re looking at DNA from an individual organism’s perspective; what is this DNA doing for me? Maybe it’s not doing anything for you, yet it exists. The purpose of DNA is simply to exist, or rather, to replicate itself from one individual into the next via replication, and so on and so on. Each individual plant, animal, or cell is just a survival machine for a group of interlinked DNA molecules to replicate themselves into the next generation (and perhaps reassort themselves along the way). A large portion of your DNA might just be ‘along for the ride’, kind of like viral DNA which jumps into and out of cells, but rather than by taking a viral vector, taking the more traditional cellular or organismal replication vector, along with the DNA that codes for the proteins that make that process possible. DNA doesn’t care about anything, it simply is. As long as the ‘junk DNA’ doesn’t exert a significantly negative affect on the whole package (be it cell or organism’s) ability to survive and replicate, that junk DNA has fulfilled its purpose: to exist, or rather, to continue to exist. It simply is.

    • ncovington89

      Oh yes, that’s very true. I believe there’s something called “long repeating elements” which act as you describe, and basically only exist because they have succeeded in making lots of copies of themselves. Either way, though, I would still classify them as ‘junk’ because they don’t contribute to the reproductive success of the organism whose genome they inhabit.