stormsewer (![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png)
stormsewer) wrote2019-01-13 04:11 pm
stormsewer) wrote2019-01-13 04:11 pm
Entry tags:
Thank Your Enzymes
Enzymes are cool. There's lots of reasons why. Strings of amino acids that fold up automagically [1] into nanomachines that carry out plethorae of crazy amazing chemical reactions in water at room temperature, it's hard for me to imagine a more astounding piece of tech. We've still only scratched the surface in figuring out how that happens [2]; biology is over the river and through the woods beyond us in terms of technical chops.
But today (as on many days), I'm thinking about thermodynamics, particularly the Second Law of Thermodynamics, which states that whatever happens, the disorder of the universe must increase. Sooner or later the stars will poop out, the planets will 'splode, everything you love and cherish will be torn into its smallest constituent pieces [3].
It can look like the complex order of our bodies and our ecosystems goes against the Second Law, but it doesn't. We only get all this structure by releasing an equivalent amount of disorder, plus interest, back into the universe. Carnivores tear apart numerous herbivores to maintain their order, herbivores shred countless plants for theirs, and even the pacifist kumbaya plants spend their days riding the wave of our sun's long-drawn death spiral in order to rip screaming electrons from their watery cradles, releasing as a by-product one of the most destructive chemical compounds known to science [4]. All of us are going deep into thermodynamic debt to keep this monkey show going, and the Second Law always sees its debts paid.
Anyway, enzymes. One of the things they drill into you in a biochemistry course is that enzymes are catalysts, which means they do not cause chemical reactions to happen, they merely allow them to happen faster than they otherwise would. Technically, thermodynamically, in God's Time, enzymes simply let things happen, they do not actively make things happen.
But practically speaking, it's not true that enzymes don't make things happen. As an object lesson (the one that inspired this post, in fact), when we were at a restaurant recently, my nine-month-old son knocked a glass out of his dear mother's hands, whereupon it moved immediately to the floor and divided itself into lots of tiny slicey bits that hastily spread themselves across the restaurant floor like a sprinkling of new snow. It was as if this glass had just been, like, waiting for the right opportunity, and was so happy to finally fulfill its destiny that it just couldn't contain itself.
So, thermodynamically speaking, my son did not cause the glass to break. That glass was gonna break sooner or later, hell or high water, gods and demons be damned, literally written into the fine print of the universal contract [5]. Entropy's Little Helper that he is, all he did was catalyze it, make the inevitable immediate. Like an enzyme.
That being technically true, kid, you did just break that glass, and now this burst of disorder is threatening to escalate even further by randomly shoving itself through the previously intact flesh of any unsuspecting meat matter that happens to pass by, unless someone makes an extra special supplemental contribution of energy to make it all go away [6].
Likewise, I say that the role of enzymes as thermodynamic traffic cops means they do make things happen. Sure, the glucose in my Chocolate Frosted Sugar Bombs was nearly screaming with impatience to kamikaze itself apart and was only too happy to finally get to live its truth, but it's glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, pyruvate kinase, and their buddies who skim a finder's fee off the top in order to keep me in the lifestyle to which I've become accustomed [6]. Meanwhile, all the DNA in my cells looks on hungrily, dreaming of the Day of Depolymerization, The Day When All Nucleotides Shall Be Free! My repair enzymes lean in close and whisper, gently, even lovingly, "Some day… Some day… But over my dead body." And they have the free energy to back it up (for now).
So thank you, enzymes. Without you selectively making sure things happen now or maybe not now, I wouldn't be here. Thank you for throwing energetic meat into the entropic grinder, that its hunger may not yet, not quite yet, seek to be sated on me.
Thank you.
Notes (with links)
[1] I'm already fed up with people using that word, but it is unfortunately overwhelmingly appropriate to the present use.
[2] Though Google's black box neural networks seem to be digging a little deeper, it remains to be seen how much of that digital wisdom will ever be translated into human understanding.
[3] And yet (Tangent Warning), there is reason to think that's just one part of a larger story. Like, think about the infinite future. On an infinite timeline, in the short term (meaning in the next 100 trillion years or so) everything will burn out and turn into nothingness, sure. But over infinite time everything that has a non-zero probability of happening will happen, and will in fact happen infinite times. Suns and solar systems will randomly coalesce and allow life to happen, and even the Big Bang will happen over and over again infinite times. An infinite number of times, you will stochastically appear out of the void only to immediately suffocate and freeze to death. The Cubs will win the World Series, hell will freeze over, pigs will fly, and we'll all live our same lives all over and over again, except sometimes everyone will have a solid gold toilet.
But the chances of a Big Bang randomly happening are infinitesimally small compared to the chances of, say, just our solar system randomly assembling itself, meaning the chances that we would happen to live here and now, a mere 14 billion years after a Big Bang in galaxy of 100 billion stars in a universe of at least 100 billion such galaxies, instead of on some small planet alone in an otherwise infinitely dead universe, are essentially zero. All that would seem to suggest that entropy won't increase forever, that something will rewind the clock, or hit the reset button on the computer, or just erase the entire document and start over again, or whatever. Though of course at the moment there's not much sign of that ever happening, the statistical improbability of the alternative suggests otherwise. (These thoughts were inspired by some YouTube video I watched a few years ago and can't find now, though Sean Carroll's TedTalk "Distant time and the hint of a multiverse" covers similar ground. See also "The Last Question" by Isaac Asimov.
[4] Wink wink nudge nudge, respiration sure is fun, though.
[5] It's Not Just a Depressing Idea, It's The Law!
[6] Entropy has some kind of protection racket going, I'll tell ya.
But today (as on many days), I'm thinking about thermodynamics, particularly the Second Law of Thermodynamics, which states that whatever happens, the disorder of the universe must increase. Sooner or later the stars will poop out, the planets will 'splode, everything you love and cherish will be torn into its smallest constituent pieces [3].
It can look like the complex order of our bodies and our ecosystems goes against the Second Law, but it doesn't. We only get all this structure by releasing an equivalent amount of disorder, plus interest, back into the universe. Carnivores tear apart numerous herbivores to maintain their order, herbivores shred countless plants for theirs, and even the pacifist kumbaya plants spend their days riding the wave of our sun's long-drawn death spiral in order to rip screaming electrons from their watery cradles, releasing as a by-product one of the most destructive chemical compounds known to science [4]. All of us are going deep into thermodynamic debt to keep this monkey show going, and the Second Law always sees its debts paid.
Anyway, enzymes. One of the things they drill into you in a biochemistry course is that enzymes are catalysts, which means they do not cause chemical reactions to happen, they merely allow them to happen faster than they otherwise would. Technically, thermodynamically, in God's Time, enzymes simply let things happen, they do not actively make things happen.
But practically speaking, it's not true that enzymes don't make things happen. As an object lesson (the one that inspired this post, in fact), when we were at a restaurant recently, my nine-month-old son knocked a glass out of his dear mother's hands, whereupon it moved immediately to the floor and divided itself into lots of tiny slicey bits that hastily spread themselves across the restaurant floor like a sprinkling of new snow. It was as if this glass had just been, like, waiting for the right opportunity, and was so happy to finally fulfill its destiny that it just couldn't contain itself.
So, thermodynamically speaking, my son did not cause the glass to break. That glass was gonna break sooner or later, hell or high water, gods and demons be damned, literally written into the fine print of the universal contract [5]. Entropy's Little Helper that he is, all he did was catalyze it, make the inevitable immediate. Like an enzyme.
That being technically true, kid, you did just break that glass, and now this burst of disorder is threatening to escalate even further by randomly shoving itself through the previously intact flesh of any unsuspecting meat matter that happens to pass by, unless someone makes an extra special supplemental contribution of energy to make it all go away [6].
Likewise, I say that the role of enzymes as thermodynamic traffic cops means they do make things happen. Sure, the glucose in my Chocolate Frosted Sugar Bombs was nearly screaming with impatience to kamikaze itself apart and was only too happy to finally get to live its truth, but it's glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, pyruvate kinase, and their buddies who skim a finder's fee off the top in order to keep me in the lifestyle to which I've become accustomed [6]. Meanwhile, all the DNA in my cells looks on hungrily, dreaming of the Day of Depolymerization, The Day When All Nucleotides Shall Be Free! My repair enzymes lean in close and whisper, gently, even lovingly, "Some day… Some day… But over my dead body." And they have the free energy to back it up (for now).
So thank you, enzymes. Without you selectively making sure things happen now or maybe not now, I wouldn't be here. Thank you for throwing energetic meat into the entropic grinder, that its hunger may not yet, not quite yet, seek to be sated on me.
Thank you.
Notes (with links)
[1] I'm already fed up with people using that word, but it is unfortunately overwhelmingly appropriate to the present use.
[2] Though Google's black box neural networks seem to be digging a little deeper, it remains to be seen how much of that digital wisdom will ever be translated into human understanding.
[3] And yet (Tangent Warning), there is reason to think that's just one part of a larger story. Like, think about the infinite future. On an infinite timeline, in the short term (meaning in the next 100 trillion years or so) everything will burn out and turn into nothingness, sure. But over infinite time everything that has a non-zero probability of happening will happen, and will in fact happen infinite times. Suns and solar systems will randomly coalesce and allow life to happen, and even the Big Bang will happen over and over again infinite times. An infinite number of times, you will stochastically appear out of the void only to immediately suffocate and freeze to death. The Cubs will win the World Series, hell will freeze over, pigs will fly, and we'll all live our same lives all over and over again, except sometimes everyone will have a solid gold toilet.
But the chances of a Big Bang randomly happening are infinitesimally small compared to the chances of, say, just our solar system randomly assembling itself, meaning the chances that we would happen to live here and now, a mere 14 billion years after a Big Bang in galaxy of 100 billion stars in a universe of at least 100 billion such galaxies, instead of on some small planet alone in an otherwise infinitely dead universe, are essentially zero. All that would seem to suggest that entropy won't increase forever, that something will rewind the clock, or hit the reset button on the computer, or just erase the entire document and start over again, or whatever. Though of course at the moment there's not much sign of that ever happening, the statistical improbability of the alternative suggests otherwise. (These thoughts were inspired by some YouTube video I watched a few years ago and can't find now, though Sean Carroll's TedTalk "Distant time and the hint of a multiverse" covers similar ground. See also "The Last Question" by Isaac Asimov.
[4] Wink wink nudge nudge, respiration sure is fun, though.
[5] It's Not Just a Depressing Idea, It's The Law!
[6] Entropy has some kind of protection racket going, I'll tell ya.