The kludge factory

Know what a kludge is?

Coined by writer Jackson Granholm in 1962, a kludge is "an ill-assorted collection of poorly-matching parts, forming a distressing whole."  Usually created when a person is faced with fixing something and lacks (1) the correct parts, (2) the technical expertise to do it right, or (3) both, kludges fall into the "it works well enough for the time being" category.

[Image licensed under the Creative Commons Zoedovemany, Screen Shot 2015-11-19 at 11.54.48 AM, CC BY-SA 4.0]

Evolution is essentially a giant kludge factory.

At its heart, it's the "law of whatever works."  It's why the people who advocate Intelligent Design Creationism always give me a chuckle -- because if you know anything about biology, "intelligently designed" is the last thing a lot of it is.  Here are a few examples:

• Animals without hind legs -- notably whales and many snakes -- that have vestigial hind leg bones.
• Primates are some of the only mammals that cannot synthesize their own vitamin C -- yet we still carry the gene for making it.  It just doesn't work because it has a busted promoter.
• Human sinuses.  Yeah, you allergy sufferers know exactly what I'm saying.
• The recurrent laryngeal nerve in fish follows a fairly direct path, from the brain past the heart to the gills.  However, when fish evolved into land-dwelling forms and their anatomy changed -- their necks lengthening and their hearts moving lower into the body -- the recurrent laryngeal nerve got snagged on the circulatory system and had to lengthen as its path became more and more circuitous.  Now, in giraffes (for example), rather than going from the brain directly to the larynx, it goes right past its destination, loops under the heart, and then back up the neck to the larynx -- a distance of almost five meters.
• Our curved lower spines were clearly not "designed" to support a vertically-oriented body.  Have you ever seen a weight-bearing column with an s-bend?  No wonder so many of us develop lower back issues.
• One of the kludgiest of kludges is the male genitourinary tract.  Not only does the vas deferens loop way upward from the testicles (not quite as far as the giraffe's laryngeal nerve, admittedly), along the way it joins the urethra to form a single tube through the penis, something about which a friend of mine quipped, "There's intelligent design for you.  Routing a sewer pipe through a playground."  It also passes right through the prostate, a structure notorious for getting enlarged in older guys.  C'mon, God, you can do better than that.

The reason all this comes up is that the kludging goes all the way down to the molecular level.  A study from a team at Yale, Harvard, and MIT that appeared last week in the journal Science looked at the fact that when you compare the human genome to that of our nearest relatives, you find that one of the most significant differences is that our DNA has deleted sections.

That's right; some of why humans are human comes from genes that got knocked out in our ancestors.

The researchers found that there are about ten thousand bits of DNA, a lot of them consisting only of a couple of base pairs, that chimps and bonobos have and we don't.  A lot of these genetic losses were in regions involved in cognition, speech, and the development of the nervous system, all areas in which our differences are the most obvious.

The reason seems to have to do with gene switching.  Deleting a bit of switch that is intended to shut a gene off can leave the gene functioning for longer, with profound consequences.  Often these consequences are bad, of course.  There are some types of cancer (notably retinoblastoma) that are caused by a developmental gene having a faulty set of brakes.

But sometimes these changes in developmental patterns have a positive result, and therefore a selective advantage -- and we may owe our large brains and capacity for speech to kludgy switches.

"Often we think new biological functions must require new pieces of DNA, but this work shows us that deleting genetic code can result in profound consequences for traits make us unique as a species," said Steven Reilly, senior author of the paper.  "The deletion of this genetic information can have an effect that is the equivalent of removing three characters -- n't -- from the word isn't to create the new word is...  [Such deletions] can tweak the meaning of the instructions of how to make a human slightly, helping explain our bigger brains and complex cognition."

So yet another nail in the coffin of Intelligent Design Creationism, if you needed one.  Of course, I doubt it will convince anyone who wasn't already convinced; as I've observed more than once, you can't logic your way out of a belief you didn't logic your way into.

But at least it's good to know the science is unequivocal.  And, as astrophysicist Neil deGrasse Tyson said, "The wonderful thing about science is that it's true whether or not you believe in it."

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