Tag Archives: evolution

How palindromes allowed males to exist

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If I were asked to give my two most valuable pieces of advice, they would be these: First, appreciate the near impossibility that you are alive. The atoms that make you have been through some shit; they’ve swirled as stardust, formed a hot molten planet (or crashed into one from elsewhere), boiled, compressed, and decayed to a point where they were incorporated into who-knows-what part of a who-knows-what number of a who-knows-what kind of strange prehistoric organism before they now make you, sitting comfortably at your computer marveling at my repeated usage of “who-knows-what”s. The other piece of advice? Never try to drink a beer without using your hands.

Without getting abundantly philosophical, you by all means shouldn’t exist. I ask that you, at least once daily, come to terms with this fact. Appreciate also that you can come to terms with anything at all, you big-brained multi-talented sculpture of evolution. Appreciate that other humans exist that can love you and carry out services to make you more comfortable. Appreciate pizza, because how did the universe create something so perfect?

Oh, and if you’re male, go ahead and appreciate that you exist. You theoretically should not.

In evolutionary terms, males are dispensable. The adaptive value of males is that they can mix up genes to create new combinations of traits on the off-chance that some of them can help prevent an untimely death, aid in making little ones, or allow one to be more comfortable overall. Males are gene donors. That’s basically it. Yeah, some males aid in parental care or perform tasks to aid group survival, but male uselessness is a common evolutionary motif. Male anglerfish are prime examples.

Gender in humans (along with a lot of other species) is determined by the identities of a pair of sex chromosomes contained in every cell. Both males and females possess one X chromosome, a large and gene-packed chromosome chock full of genetic goodies. Females have a pair of X chromosomes, one from the mother and one from the father. Males, however, have only one X chromosome, donated by the mother, and a shrimpy and scrawny Y chromosome donated from the father. X chromosomes contain some 2000 known genes, Y contains only 78. Bummer.

There’s a good reason why the Y chromosome is so scrawny: DNA damage is pretty common. Being so long and fragile, DNA can become knotted, coiled, unwrapped, kinked, looped, mutated, irradiated, copied wrong, fixed wrong, proofread wrong, chopped, sliced, chunked, choked, broken, inverted, doubled, misread, and misunderstood. Each of your cells possesses a SWAT team of enzymes that try to prevent these things from happening, but they’re not without error. Mistakes happen. So, because our cells possess 2 copies of each chromosome, when one becomes overly mangled, these enzymes can use the other as a template of instructions to repair the damage.

X chromosomes do this beautifully. These, in short, scan each X chromosome and check for inconsistencies, using one or the other to clear up any mismatches in DNA code. Two similar chromosomal regions can also “cross over”, exchanging segments of DNA that encode for roughly the same type of protein. Most of the time, crossing over is beneficial because it throws some genetic variety into the mix.

Crossing over is like holding hands, only after you’re done, your hands trade bodies. Good old nightmare fuel.

X and Y were once paired just as healthily as two X chromosomes are today: both were large, bountiful chromosomes that crossed over frequently and used each other as repair templates. About 300 million years ago, as reptiles and mammals diverged, a mutation caused the Y chromosome to take on more “manly” attributes, including the development of testes, sperm, different hormone production, etc. X and Y were now very different chromosomes. Crossing over ceased between them. Cellular machinery stopped using one to proofread the other. They became distinct and wary of the other. The X chromosome still had a healthy pair in females and could easily use one to keep the other functional, preserving the integrity of the chromosome.

Unfortunately, Y became a genetic desert island, left all by its lonesome with nothing to use as a spell checker in case things went very wrong with its code.

By this logic, many scientists think the Y chromosome should have been obliterated. With more and more DNA mutations accumulating, more and more of the chromosome was snipped away and discarded. To make matters worse, portions of the chromosome inverted themselves. Areas swapped information, mixing things up further. The Y chromosome was rapidly becoming giant mess. Eventually, removing all these errors caused Y to become tiny, almost biting the dust altogether and doing away with males entirely! But it’s still kicking even after 300 million years. With no partner to help proofread its DNA, how did the Y chromosome survive?

DNA and language share many things in common. Almost too many. One of them is that segments of information, called palindromes, can be read from left to right or right to left and read the same way: God, a red nugget, a fat egg under a dog! DNA contains palindromes too, and they can be long, sometimes hundreds of bases in length. The problem with DNA palindromes is that they are a liability; because bases like to chemically pair up with their counterparts, segments of independent DNA can stick together to form looped hairpins, derailing the important cellular machinery necessary for replicating, proofreading, and transcribing DNA into proteins.

Palindromes on two strands of DNA can join to form hairpin regions. These are bad. Imagine a train barreling down track shaped this way and you get the picture.

The Y chromosome in particular is full of palindromes. Normally, high palindrome density is a chromosomal death sentence. However, in the case of the Y chromosome, palindromes were a blessing. Because the Y chromosome had so much repeat information and no paired chromosome to proofread it, Y could use different segments of ITSELF to validate that the information on another segment was correct. Y chromosome palindromes kink together and use one strand to proofread the other, turning large segments of the chromosome into genetic hairpins. Because both are palindromes, one segment should read exactly the same as its folded-over counterpart. So, in a sense, the Y chromosome uses what’s normally a huge flaw as its primary means of keeping information correct.

As an added bonus, this method of palindrome proofreading can create new varieties in the DNA code akin to crossing over in X chromosomes. When one strand is damaged, the enzymes responsible for repairing it can’t distinguish the damaged strand from the undamaged one. All it can do is discriminate one from the other. Therefore, it has to guess which of the two sides needs fixing. Often, this can cause the undamaged segments of DNA to take on the information of the damaged counterpart, creating new combinations of DNA code to form. While this could possibly ruin the genetic meaning of the original, it also presents an opportunity for new traits to become expressed on the ever-changing Y chromosome.

Self-repairing Y chromosome palindromes at work. This is something I’ll surely bring up at the table come Thanksgiving.

I cannot over-emphasize how important palindromes are to the sustainability of the Y chromosome. Without this ingenious little method, human history would have played out very differently. So, while palindromes can be a fun way to parody a Bob Dylan tune, be thankful that they also keep you healthy and keep your identity in check. Add that to your list of things to appreciate.

A special thanks to Sam Kean, whose book “The Violinist’s Thumb” encouraged me to write this article. It’s a fantastic read, I highly suggest it.

For more information:
http://phylogenous.wordpress.com/2010/10/01/y-chromosome-vii-why-palindromes/

http://www.hindawi.com/journals/ijeb/2012/207958/

 

Humanity’s Most Badass Adaptation II: Sucks to be small

Why Ant-man is the worst superhero ever.
What if we were much smaller? Well, there’s good and bad news. The good news is that we could adopt simpler body forms, but that’s about it. The bad news? Pfft.

First. we would probably be much dumber than we are. Zoom in closely on the brain of every animal and you’ll find neurons, cells that communicate to one another using electrical or chemical signals. Hundreds to thousands of these neurons form dense and complicated circuits with one another in the vertebrate brain. Such circuits form pathways that tend to perform specific functions in the body. For instance, there are specific regions of the brain designated for movement, for regulating sleep, for hunger, for balance, for typing “guns and missiles”, and for interpreting the sights, sounds, and smells from the world. Our bodies may be able to shrink in size and still function to some degree, but our neurons cannot only be miniaturized and still function with such complex synchrony and elegance. As we grow significantly smaller, we run out of room for neurons very rapidly.

“But Kevin, I’ve always heard that a big head doesn’t mean make you smarter”. Don’t you sass me. But you are right, anonymous naysayer. There is admittedly weak evidence that intelligence correlates with head volume, yes, but that’s among humans of relatively the same size [3]. For example, my fiancée is tiny and adorable, though she’s likely smarter than I am (Fiancée et al, 2014). However, when we’re talking about a difference in scale between us and a mouse, size matters. We have nearly half the number of neurons as the U.S. military has guns and missiles, something around 86 billion neurons [5]. Mice have around 10 million. Ants have around 200,000. To put this into perspective, if each neuron were a person, our brains would outnumber earth’s human population 12 times over. A mouse’s would be constrained to the size of North Carolina. An ant’s would be Laredo, Texas. It’s hard to grow intellectually when you’re Laredo, Texas.

I apologize to anyone from or living in the city limits of Laredo. I did not mean to say your city is dumb. However, it certainly looks that way. I’ve visited your website. It looks terrible.

Come to Laredo and visit our…moon.

Being the size of an insect would present a number of other challenges. The interactions we have with things in our environment (like the water we drink and the food we eat) conform to the laws of physics. As we shrink in scale, these interactions change. To an ant, water seems as viscous as maple syrup. Gravity takes a backseat to air turbulence. As Steven Jay Gould writes, “An ant-sized man might don some clothing, but surface adhesion would preclude its removal. The lower limit of drop size would make showering impossible; each drop would hit with the force of a large boulder. If our homunculus managed to get wet and tried to dry off with a towel, he would be stuck to it for life. He could pour no liquid, light no fire…” [2].

Could an ant-sized version of early man have developed civilization even if intelligence were not a factor? Probably not, at least not at the same rate or with the same level of success. I imagine cultivating agricultural crops, one of the supposed precursors for civilization, would have been near impossible, not to mention cross-breeding them for good yield. Our meat-based diet would be replaced with who knows what, but I suppose it would include plant material and any nearby organism that decides to die. For that matter, hunting would be folly; spears and bows would be completely ineffective because we probably couldn’t put enough force behind the blow. Guns and missiles wouldn’t exist. Our predators would vastly rise in number, distancing us from the top of the food web. We’d be stomped into submission by the elements, by other creatures, and by our own ineffectiveness. Switzerland would be near impossible to get to. So long, Mürren.

What about food? Shouldn’t food be more abundant since, you know, one kernel of corn could feed an entire village of people? That’s true, but there’s a much bigger caveat to this than you’d think. The world’s food is spatially patchy. I don’t just mean that bananas only grow in the tropics or that rice grows best in silty soil. I mean that, when you’re the size of an ant, getting a bug from the ground nearby is a marathon. Food sources are really f**king far apart, but plentiful once they’re found. Many animals that live upon such food sources adopt life strategies to cope with smorgasbord-style resources. Some insects that exploit huge but infrequent foods, including flies like the gall midge, have adaptations that allow them to exploit them quickly. Gall midges typically reproduce sexually, though it takes a long time for larvae to develop this way. When midges find a mushroom, a gold mine on their scale, females reproduce without a male through a process called parthenogenesis. These offspring are formed more quickly than doing things via the sexual route, though it comes at a cost to the mother. Instead of developing externally, the larvae grow inside the mother, eventually liquefying her insides and bursting from her lifeless husk [4]. However, immature as they may be, they are ready to start chomping away on some sweet sweet mushroom bits and rotting parts of their mommah. D’awww. Overall, the flies have more successful babies this way, thus the need for bursting out of their moms and such.

Will humans do that? I dunno. That sounds desperate. But food would likely be lacking for most humans on earth. Maybe we’d be as successful as ants and develop complex chemical signals to communicate the locations of food, bypassing any other weird adaptations like the ones midges have . Maybe we wouldn’t, and we’d fill just another tiny niche in the complex world which we inhabit.

So, I hope you now understand how important our size is for our survival. We are big and scary creatures, and that’s allowed us to hunt and kill and eat meats and make pizzas and build guns and missiles. But we’re not so large that joint damage, eating entire herds of cattle per day, and toppling over and breaking bones would be a daily norm. We’re also not so small either that we can’t take showers or cultivate food. So, here we stand, results of the goal-less, powerful, yet delicate hands of natural selection. Just right.

Nobody comments on my stuff. You should comment on my stuff. Get your friends to comment on my stuff. I will then comment. We can all comment. It will be a great world full of comments.

WE HAVE GUN AND MISSILE CONFERENCES!!! HUMANITY, BITCHES!!!

 

Literature Sources:

[1] http://en.wikipedia.org/wiki/Kleiber’s_law

[2] “Ever Since Darwin” by Steven Jay Gould, Norton & Co. 1977

[3] http://science.howstuffworks.com/life/inside-the-mind/human-brain/brain-size2.htm

[4]http://www.sjgarchive.org/library/text/ontogeny/p0306.htm

[5] http://journal.frontiersin.org/Journal/10.3389/neuro.09.031.2009/full#B24