Like your big brain & non-spiny penis? Thank "junk" DNA.

Noncoding DNA is a weird thing. This is the stuff that's often called "junk" DNA, because it's not involved in making protein sequences—the building blocks of life. But, just because noncoding DNA isn't part of our genetic bricklaying crew, that doesn't mean it's not involved in the construction project. There's a growing body of evidence, from many different researchers, that suggests "junk" DNA might be pretty important stuff. In fact, a recent paper in the journal Nature claims that changes in noncoding DNA have been responsible for some of the important physical characteristics we humans enjoy today.

Like, say, for instance, the fact that the penis of the human male is not spiny. Megan Scudellari at The Scientist explains:

For over a decade, Kingsley's lab has studied the genetic basis of evolution in stickleback fish, and found time and again that major morphological differences can be tracked to deletions in regions of DNA surrounding key developmental genes. To see if the same was true for human evolution, Kingsley and colleagues compared the human and chimpanzee genomes, identifying 583 human-specific deletions. They then narrowed the list to sequences likely to have an important function by looking for those which are highly conserved across other organisms, including rhesus macaques, mice, and chickens.

The team's final list included 510 DNA deletions, highly conserved across animal species but absent from the human genome. All but one of the deletions mapped to non-protein coding regions, and many were near genes involved in steroid hormone signaling and neural function.

The team closely analyzed two of the deletions and their potential contribution to human evolution. One, a deletion near tumor suppressor gene GADD45G, may have removed the brakes from cell division and promoted the expansion of brain tissue, contributing to the increase in brain size of humans over other primates. A second, a deletion near the human androgen receptor gene, correlates with the loss of sensory whiskers and penile spines, which mice and other primates still have, but humans (thankfully) lack.

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Maggie Koerth-Baker is the science editor at BoingBoing.net. She writes a monthly column for The New York Times Magazine and is the author of Before the Lights Go Out, a book about electricity, infrastructure, and the future of energy. You can find Maggie on Twitter and Facebook.

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Brainspore

I wonder if this implies anything about the brain size of people who augment their penises with spines.
silkox

Are we talking about internal or external spines? One we’re probably better off without; the other maybe some of us would prefer to have returned to their rightful owners: OS PENIS, CONGENITAL ABSENCE OF (all caps in original).
rebdav

In cats the penile spines are responsible for stimulating ovulation, I suppose it is the closest that female cats get to an orgasm. It sure makes them damn noisy.
- benher
  
  Unfortunately for my little female feline, not getting any also makes her noisy… Maybe I should invest producing some sort of franken hybrid cactus/catnip thing.
  Junk DNA be damned! Let our grandkids deal with the consequences!
  - Datura Greenleaf
    
    Has your cat been spayed? If not, she really should be!
Ito Kagehisa

There is no such thing as “junk” DNA.

I used to get in that argument all the time 20 years ago. Generally, I won by having a higher tolerance for alcohol than the geneticists, rather than by convincing them to study information theory. This is one of several reasons why I often prefer to have scientific arguments in bars.
- Anonymous
  
  I have studied information theory, Kolmogorov complexity, and genetics, and you, sir, are full of it.
kenmce

The obvious thing to do is to work up some mice or something that have had all the “junk” DNA removed from their genome. Grow some and see if they’re viable. Some of it might just be unused leftovers, or cross species relics, but my suspicion is that some of it is doing something, because nature likes parsimony.
- travtastic
  
  I read an article about that happening a while ago, but I don’t remember if they did it on purpose.
  
  Apparently some of the non-coding DNA was being triggered by other genes and environmental factors.
  - travtastic
    
    Which I guess means ‘non-coding’ is probably a bad term to use. ‘Disabled’, I guess.
Anonymous

Something to remember, though, is that there is a ton of non-coding DNA. A little of it has turned out to be useful, maybe as much as coding DNA, but the vast majority still has no known function, to such a great extent that a lot probably truly doesn’t have any.
Aurophobia

No, “junk” DNA refers to the huge gene deserts in the genome that don’t even have regulatory elements. Also included are the foreign non-functioning viral genomes that got integrated into our genome long ago. Only a tiny percentage of our genome codes for proteins.

The ENCODE Project is working to map all of the regulatory elements in the human genome as we type.
Datura Greenleaf

I don’t know, sensory whiskers might be cool!
pauliswhoiam

This is really dissapointing that “Junk DNA” has been confused with non-coding DNA. It’s perfectly clear to geneticists that a proportion of non-coding DNA is involved in regulation. When they refer to “Junk DNA” they’re talking about the vast sequences for which there is no conceivable function. They can not conceive of a function because all the evidence points to there being no function at all, not because they sit in ivory towers. For example, genome sizes vary enormously between species, even some closely related species, despite the fact that nothing different in their phenotypes would necessitate this. This is elegantly expressed in the onion test: http://pandasthumb.org/archives/2007/06/junk-dna-junk-s.html
Put simply, onions have 5 times more non-coding DNA than us, and the most plausible explanation for this is that the majority of it does nothing at all.
Nature doesn’t like parsimony; natural selection may favour parsimony, only if it’s technically possible and if it makes a difference to reproductive fitness. But evolution is not a progression towards ever more elegant solutions to living, it’s way more messy.
The way DNA sequences work, they can pointlessly repeat themselves on the genome, and during reproduction these pointless copies will be faithfully reproduced in a whole load of generations after that, perhaps until they are just as accidentally deleted. Also, as mentioned, retroviruses can sneak into the genome and add to the junk. The fact we are carrying loads of junk DNA (in common with so many other organisms) doesn’t significantly affect our reproductive fitness, so natural selection doesn’t get a say in the matter.
Natural selection is not the entire story of evolution, although that is all too often how it is taught.
The GMO opponenents who assume this sort of story is proof of genetecists’ ignorance are making the wrong assumptions. Although there may be some details still to learn, GMOs are well understood and rigoruosly tested. This entire study was based on transgenic mice, like so many other studies in genetics.
GM is incredibly useful, and the fact that it’s been monopolised in many cases by disreputable agribusiness says nothing of the technology itself. The precautionary principle, arguing that unknown risks or very small risks should halt technological progress is untenable in my opinion, what with our growing, quarter-starved world…
- Anonymous
  
  They can not conceive of a function because all the evidence points to there being no function at all, not because they sit in ivory towers.
  
  Logically and scientifically, that is utter nonsense, and self-disproving nonsense at that.
  
  If they weren’t sitting in ivory towers, they’d call it DNA they don’t understand. Instead they call it “junk”. There is no such thing as evidence that points to not-evidence. If it points to something that has no known meaning, the pointer itself is nothing but partially resolvable metadata.
Ipo

A “boner” would seem to make viagra superfluous.
From silkox link:
Gilbert and Zevit (2001) suggested that it was not a costal rib but rather the penile ‘rib’ or baculum that God removed from Adam to create Eve (Genesis 2:21-23). Genesis also states that ‘the Lord God closed up the flesh.’ Gilbert and Zevit (2001) suggested that the raphe on the penis and scrotum was thought to be the surgical scar.

God: “It’ll cost you an arm and a leg.”
Adam: “Hmm, what can I get for a rib?”
phosphorious

But what if you like penile spines?
- Antinous / Moderator
  
  Once you go demon, you never go back.
  - travtastic
    
    I’m so tired of women always hogging all the good genital dentatas.
- Bill Albertson
  
  Dydoes, and maybe a frenum or two.
- millrick
  
  functional or ornamental?
Anonymous

I’m beginning to think that “vestigial organ/limb,” “junk DNA,” and “Quantum Physics” are just scientist code for, “We have no idea what’s really going on here.” Just because you don’t know something doesn’t mean it isn’t very important.
- Anonymous
  
  Vestigial limbs are sometimes known to be important, just reduced, but there are cases where they have been known to disappear entirely. And quantum physics is actually quite well understood, except when you try to combine all the forces, or when you try and use it to sell healing salves. If you’re getting the impression otherwise, start looking at actual journals.
pumuckl

Non-coding DNA is also important for transcriptional and translational regulation, though that’s been known for a while.
Anonymous

I think this is part of the reason that so many people are opposed to GMO food. We *don’t know* what we are doing when we are tinkering with DNA to produce hybrid organisms. I have heard the phrase “junk DNA” bandied about in conferences where this sort of thing is discussed – its not just journalistic laziness.

“Junk DNA” = I don’t know what it does so it cannot be important.

This story and others like it prove that once more, some scientists have made the error of all-knowing arrogance and are more than happy to risk other folks and the environment on the wager that they have a complete understanding. DDT anyone?

Noncoding DNA does make a difference, as per story above, so when its ignored we do not know what the results will be – what may be modified. Now, I don’t *expect* GMO wheat to start doing something unexpected BUT we don’t know. And this is one of the Rumsfeltian unknown unknowns – our understanding of this stuff is still incomplete (aka “Junk DNA”) – so we really just don’t know what could crop up.

Since GMO food organisms seem to be the lovechild of Big Business and Ivory Tower arrogance, lets at least wait until we have a more complete picture of how stuff works before releasing it into the wild . . .

Anti-science? No, I don’t think so. Anti-ignorance, if anything.
- Anonymous
  
  I wouldn’t characterize your position as either anti-science or anti-ignorance, but fear-based ignorance. You seem to be taking the position that if we do not fully know the consequences of some action, then the action should not be undertaken. Sometimes, the consequences of an action can only be known by performing the action. Someone probably once said, “don’t try to split the atom, we don’t know what will happen.” We did it anyway, and now know what will happen if we act irresponsibly with the knowledge we gained. There is nothing to be gained by cowering in fear of the unknown.
- Wormman
  
  “I think this is part of the reason that so many people are opposed to GMO food. We *don’t know* what we are doing when we are tinkering with DNA to produce hybrid organisms. I have heard the phrase “junk DNA” bandied about in conferences where this sort of thing is discussed – its not just journalistic laziness.”
  
  Except that the genes that are transferred in GMOs tend to be just the coding bits, with the non-coding bits chopped out for convenience, so any talk of “junk DNA” really doesn’t apply here.
  
  Human beings have been messing about with the genomes of other species for thousands of years. If we’re going to start worrying about it just because we can do it in a few weeks to months rather than over generations, then I think that is an “anti-science” viewpoint.
  - travtastic
    
    That really is a ridiculous argument. Artificial selection over 5,000 years is not the same thing as genetic engineering in a laboratory.
    
    There’s the time frame for finding and correcting mistakes. There’s cross-contamination from horizontal gene transfer. IP restrictions, including hard-coded auto-sterilization genes to force third-world farmers to pay for seeds year after year. Monocultures and their susceptibility to rapid die-offs. The unintended disruption of native ecosystems.
    - pauliswhoiam
      
      Unintended disruption of natural ecosystems is a feature throughout the history of agriculture, not just with GMO
      - travtastic
        
        Seriously? No they don’t. That’s silly.
    - Wormman
      
      “There’s the time frame for finding and correcting mistakes. There’s cross-contamination from horizontal gene transfer.”
      
      Yep – I’ll give you those two. There are quite a few other things that should be taken into account as well. One which is more relevant to this topic is how those genes we are transferring rely on regulation by the non-coding bits we don’t transfer. However . . .
      
      “IP restrictions, including hard-coded auto-sterilization genes to force third-world farmers to pay for seeds year after year.”
      
      These arguments are to do more with the behaviour of large multinational corporations rather than the science involved. I never said that the way we are handling GM is sensible or moral. I’ll criticise the appalling actions of Monsanto and the like with the best of them. My objection is to the kneejerk rejection of GM because of reasons which aren’t unique to GM. As a case in point . . .
      
      “Monocultures and their susceptibility to rapid die-offs. The unintended disruption of native ecosystems.”
      
      Both of which have been happening for the thousands of years since humans starting farming. My point is that many of the opponents of GM don’t seem to have as much of a problem with monocultures dying off or destroying native ecosystems so long as traditional breeding methods were used to create those monocultures. These things are a problem due to our farming activities, not the provenance of the organism, yet you don’t see activists destroying traditional farms.
      
      GM needs to be carefully regulated. The side effects of transferring genes need to be examined before they are unleashed and an understanding of the way the coding section of the genome interacts with the non-coding component is an important step in doing this. The last people who should be responsible for this are self-regulating, profit-driven corporations with a vested interest in not being transparent about their processes.
      
      It should also be pointed out that GMOs are more stringently tested before release than any other new food product (particularly traditional produced hybrids). There are more controls placed on GMOs than the average produce from your local organic food coop.
      
      My clumsily worded response to the original post was merely pointing out the silliness in trying to use “we don’t know about non-coding DNA” as a reason why people fear GMOs. Our ancestors didn’t know all the effects of hybridising the root stocks which led to our current crop of crops, but I’m kind of glad they made that great leap into the unknown.
      
      There is much valid criticism of GM, but most of it can be put down to the bad behaviour of the people we’ve trusted to do it, rather than the concept itself. Most of the rest of the criticism can be boiled down to the almost religious position of “we shouldn’t mess with nature”, which is irrational since we’ve been doing it for thousands of years anyway.