Chemistry

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There may be no firm fundament but is there a fun firmament?

It’s Tuesday morning, now, and I’m writing this on my laptop computer, mainly to spare my thumbs, but also because I just prefer real typing to the constrictive and error-ridden twiddling of virtual buttons on a very small phone screen.

Speaking of the day, if the Beatles song Lady Madonna is correct, then it’s still Tuesday afternoon, and has been at least since last Tuesday, since “Tuesday afternoon is never-ending”.  Of course, if Tuesday afternoon really is never-ending, then it has been Tuesday afternoon ever since the first Tuesday afternoon.  From a certain point of view, this is trivially the case.  After all, every moment after 12pm on the first Tuesday that ever happened could be considered Tuesday afternoon—or, at least, they could be considered “after Tuesday noon” if you will.

Enough of that particular nonsense.  I only wrote that because there’s nothing sensible about which to write that comes to my mind.  But, of course, in a larger sense, there is nothing “sensible” at all.

There are things that can be sensed, obviously.  I can see, hear, and touch this computer, for instance.  If I wanted, I could probably smell it, though I think its odor is likely quite subdued.  But I mean “sensible” in the more colloquial, bastardized, mutated sense—as in the word “sense” just there—which has to do with something being logical, reasonable, rational, coherent, that sort of thing.  Indeed, it has to do with things having meaning.

Deep down, though, from the telos point of view, there is no true, inherent meaning to much of anything, as far as anyone can see.  Certainly there’s no meaning that anyone has ever demonstrated or asserted convincingly that I have encountered at any point in my life.

Of course, people have beliefs and they have convictions, and humans assign meanings to various things.  All the words I have used in writing this post so far, and all the words I will use henceforth, have “meanings”, but those are invented meanings.  There is nothing in the collection of letters—nor indeed in the shapes of the letters themselves, nor the way we put them down on paper or a screen—that means anything intrinsically.  They were all invented, like justice and morality and the whole lot of such things.

That something is invented doesn’t mean it isn’t real, of course.  Cars are an invention, and only a fool (in the modern world) would deny that cars are real.  But they are not inherent to the universe; they are not in any sense fundamental.

In a related sense, even DNA and the protein structures for which it codes are very much not fundamental; they are quasi-arbitrary.  Of course, one cannot make DNA or RNA or proteins out of substrates for which the chemistry simply will not hold together.  But the genetic code—the set of three-nucleotide-long “letters”, the codons, in the genetic code that each associate with a given amino acid (or a stop signal, or similar) as they are transcribed into proteins—is arbitrary.  There’s nothing inherent in any set of three nucleotides that makes it associate with some particular amino acid.

This sort of thing took me quite a long time to realize as I was growing up and trying to understand biology and chemistry and such.  What, for instance, was the chemical reaction with, say, adrenaline that made things in the body speed up and go into “fight or flight” mode, as it were?  How was it that aspirin chemically interacted with bodies and nervous systems to blunt pain?  How many possible chemical reactions were there, really?  It was mind-boggling that there could be so many reactions, and that they could all produce such disparate effects on various creatures.

When finally I was shown the real nature of such things, it was definitely a scales-dropping-from-eyes moment.  There is nothing inherent in the chemistry of DNA, or of drugs or hormones, that produces their effects.  There is no inherent “soporific” quality to an anesthetic.  You could give a dose of Versed  that would kill a human to some alien with a different biology, and at most its effects would be those of a contaminant.

It’s all just a kind of language—indeed, it’s almost a kind of computer language, and hormones are just messengers*, which are more or less arbitrary, like the ASCII code for representing characters within computer systems.  Likewise, there’s nothing in the word “cat” that has direct connection with the animal to which it refers.  It’s just keyed to that creature in our minds, arbitrarily, as is demonstrated by the fact that, for instance, in Japan the term is “neko” (or, well, it sounds like that—the actual written term is ねこ or 猫).

Of course, there are things in the universe that, as far as we can tell, are fundamental, such as quantum fields and gravity and spacetime itself.  But even these may yet peel away and be revealed to be arbitrary or semi-arbitrary forms of some other, deeper, underlying unity, as is postulated in string theory, for instance.

The specific forms of the fundamental particles and forces in our universe may—if string theory and eternal inflationary cosmology for instance are correct—be just one possible version of a potential 10500 or more** possible sets of particles and forces determined by the particular Calabi-Yau “shape” and configuration of the curled up extra dimensions of space that string theory hypothesizes.  So, the very fundamental forces of nature, or at least the “constants” thereof, may be arbitrary—historical accidents, as much as are the forms and specifics of the life that currently exists on Earth.

And what’s to say that strings and branes and Calabi-Yau manifolds are fundamental, either?  Perhaps reality has no fundament whatsoever.  Perhaps it is a bottomless pit of meaninglessness, in which only truly fundamental mathematics are consistent throughout…if even they are.

I’m not likely to arrive at a conclusion regarding these matters in a blog post written off-the-cuff in the morning while commuting to the office.  But I guess it all supports a would-be Stoic philosophical ideal, which urges us to let go of things that are outside our control and instead try to focus on those things over which we have some power:  our thoughts and our actions.

Of course, even these are, at some deeper level, not truly or at least not fully ours to control—we cannot affect the past that led to our present state, after all, and the future is born of that present which is born of that past over which we have no control.  But, for practical purposes, the levers that we use to control ourselves are the only levers we have to use.

We might as well keep a grip on them as well as we can, and not worry too much about things that are not in our current reach.  Though we can try to stretch out and limber up, maybe practice some mental yoga, to try to extend that reach over time, I suppose.  But that’s a subject for some other blog post, I guess; this one has already gone on long enough.

*For the most part.  Things like cholesterol and fatty acids and sugars—and certainly water and oxygen—and other fundamental building blocks do have inherent chemical properties that make them useful for the purposes to which bodies put them.  Then again, words can have tendencies that make them more useful for some things than others, too.  “No” and “yes” are short and clear and clearly different sounds, for instance; it makes sense that such words evolved to be such important, fundamentally dichotomous signals.

**That means 10 x 10 x 10 x 10… until you’ve done that multiplication 500 times.  You may know that a “googol” is a mere 10100, and that in itself is already roughly 20 orders of magnitude (100,000,000,000,000,000,000 times!) larger than the number of protons and neutrons estimated to exist in the visible universe.  So 10500 is a number far vaster than could ever be written out within the confines of the universe that we can ever see.  There’s not enough space, let alone enough matter, with which to write it.  It’s a googol times a googol times a googol times a googol times a googol!

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Believing in “believing in” matters of empirical reality…or not

The other day, I was scrolling through The Website Formerly Known as Twitter—which I tend to do after sharing my blog posts there, since it seems the polite thing to do—and I saw a “tweet” or an “X-udate” or “X-cretion” or whatever one calls them now, that asked, “Do you believe in global warming?”

Such questions always seem bizarre to me.  It’s similar to the old, “Do you believe in UFOs?”  Though, with the latter, one can always snarkily reply, “Why, yes, I believe in unidentified flying objects.  I think people often see things in the sky that they cannot properly identify, especially if they are not experts and conditions are not ideal.”  But really, even that sarcastic response misses the point and can be misleading, so it’s best to be avoided.

The problem is, the question entails a kind of category error.  The reality of global warming—by which I assume the questioner means some form of anthropogenic climate change—is an empirical question.  It is a statement about reality itself, and is either true or false whether or not anyone even knows about it as a possibility, let alone “believes in it”.

It’s more reasonable to ask, “Do you believe that anthropogenic climate change—AKA global warming—is happening?”  That, at least, is a sensible question, when using the form of the word “belief” that means that, based on the evidence and reasoning one has available, one has arrived at the provisional conclusion that global warming is happening (or is not).

In using this term “belief”, one would usually imply that one is reasonably convinced, but open in principle to alternative explanations and counter arguments and new evidence—as one always should be in matters of empirical fact, at least if one is committed to always trying to make one’s map describe the territory as well as possible (to borrow a phrase from Eliezer Yudkowsky).

But when people say, “Do you believe in…” something, it doesn’t come across—to me at least—like a question about facts, but rather as a question about ideologies, about team membership, about religion, in a way.  It can be at least excusable and appropriate, if still rather nonsensical in my view, to ask someone if they believe in Santa Claus, or in Communism, or in God.  It doesn’t necessarily have anything to do with external reality other than the state of certain people’s minds, but at least it’s reasonably appropriate.

The absurdity of this conflation of “believing in” something with an assessment of a thing’s actual reality is pointed out well in Terry Pratchett’s delightful Discworld novels—in either Wyrd Sisters or Witches Abroad, if memory serves.  I don’t recall how the point comes up, but it relates to belief in the gods of Discworld.  The narration says that, of course, witches knew that the gods were real, they had dealings with them, they sometimes met them.  But that didn’t mean there was any call to go believing in them.  It would be like believing in the postman.

If someone were to ask me whether I think that climate change is real, and why I think whatever I think, I might reply that the general consensus of the world’s climate scientists—people who actually specialize in the area—seems to be that it is happening, and though their most specific predictions can be highly uncertain, as can all specific predictions in science beyond the realms of simple linear dynamics, most of them conclude that it is really happening.

I read a statement once that claimed that the percentage of climate scientists who are convinced that human-caused global warming is really happening is higher than the percentage of medical scientists who are convinced that smoking tobacco increases the risk of lung cancer.  I don’t know whether that statement is true, and I don’t recall the source—it sounds more like a rhetorical point than an actual argument, which makes me suspicious.  If it is true, it’s remarkable in more than one direction.

One can look up in journals the papers and the data that is being gathered and analyzed by climate scientists.  Google Scholar works nicely for searching out real, published scientific studies on almost any amendable topic.  One can also go to pre-print servers such as arXiv, to see papers that have not yet been peer reviewed.

If one is judicious, one can even find decent science news in less technical publications—phys.org seems to be pretty good—but mainstream reporting on such things is often unreliable and inconsistent, since after all mainstream media exist primarily to sell themselves, not necessarily to promulgate the most rigorous truth they can uncover.  Even Scientific American has turned into a twisted mockery of its former self.

I understand at least some of the physics behind the “greenhouse effect”, without which the Earth would be uninhabitably cold.  Visible light passes through the atmosphere without interacting much with the gases therein—which is why air is mostly transparent, other than the modest scattering of blue light that leads to the sky’s daytime color (and inversely to the color of sunsets).  But such relatively low-entropy, high frequency light is absorbed by the ground, then reemitted as higher entropy, lower frequency light, such as infrared, which is much more readily absorbed by molecules like CO2 and H2O and methane (CH4).  The reasons for this are quantum mechanical in nature, but the fact that it happens is basic physics that’s been well known since before anyone currently alive was born, as far as I know.

And so, these atmospheric gases heat up (and in turn heat up the other atmospheric gases) until the outer surface of the atmosphere is warm enough to radiate out as much energy as comes into the Earth.  Such is the nature of so-called black body radiation.

But for the outer atmosphere to be warm enough to do this, the middle atmosphere must be warmer, and the layer below warmer still, and so on, since outer layers radiate inward as well as outward.  The outer layer of the atmosphere will always be just warm enough to radiate out just as much energy as the Earth receives in light from the sun; if it were not, the Earth would rapidly get hotter until a new equilibrium was reached.  The final radiating surface might end up being higher in the atmosphere, which would mean that, closer to the surface, things would be warmer.

Anyone who has dressed in layers in cold weather should understand this intuitively.

[By the way, there may be some slight imprecisions in my very quick summary above of the thermodynamics of atmospheric gases, so if any experts in the matter would like to make any corrections—especially if such corrections are truly substantive—please feel free to do so in the comments.]

There are other atmospheric effects that are even easier to understand at basic chemical levels, such as the fact that increasing CO2  concentration leads to increasing acidification of the oceans.  This is fairly straightforward chemistry—carbon dioxide, when dissolved in water, partially reacts to form a weak acid—“weak” meaning just that the hydrogen ions do not completely dissociate from the molecule H2CO3*.  This can be demonstrated easily by getting some pH paper (readily available at all high street pH paper shops), testing some neutral water (to confirm its baseline neutral pH) and then blowing through a straw into the water for a few minutes.  You can then check if the pH has dropped, which—if you are a typical mammalian creature from Earth—it will have done.

I think this experiment can also be done with phenolphthalein, which is wine-red when in a basic (alkaline) solution and clear when in an acidic environment.  You can do a sort of magic trick, turning “wine” into “water” with just your breath through a straw bubbling in a glass.  Don’t drink it, though.  I don’t think phenolphthalein is particularly dangerous, but I wouldn’t want to endorse someone imbibing it.

I’m not going to tell you my conclusions about the empirical fact of whether or not “global warming” is happening and how and why and all that.  You can explore the subject as a homework assignment (but don’t hand it in to me).  But I will tell you my conclusion, which is probably obvious, about “believing in” things.  I don’t believe in “global warming” nor in the lack thereof.  I don’t believe in Santa Claus.  I don’t believe in Capitalism or Communism or Socialism or Fascism or Scientism** or Antidisestablishmentarianism.  I don’t believe in the Tooth Fairy, and I don’t believe in life after love.

And I really don’t believe it’s useful or good or anything but an irrationality to “believe in” matters that involve claims about the nature of reality itself.  Reality is that which exists whether or not anyone believes in it—indeed, whether or not anyone exists to be capable of believing in it.  That’s why it’s reality, as opposed to fictions and ideologies and other abstract concepts of various kinds.

I know*** that Amazon delivery people exist.  That doesn’t mean there’s any call to go believing in them.

* H2O + CO2 ⇌ H2CO3 ⇌ H+ + HCO3–.  Something like that, anyway.

** Though I have more sympathy for Scientism than most “isms”.

***Not to a mathematical certainty, but to such a high degree that there’s no clear point in considering other possibilities, pending new evidence and/or arguments.

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The sweetest honey is loathsome in its own deliciousness. And in the taste destroys the appetite. Therefore, blog moderately.

Hello and good morning.  It’s Thursday again, so I return to my traditional weekly blog post, after having taken off last Thursday for Thanksgiving.  I’m still mildly under the weather, but I’m steadily improving.  It’s nothing like a major flu or Covid or anything along those lines, just a typical upper respiratory infection, of which there are oodles.  Most are comparatively benign, especially the ones that have been around for a while, because being not-too-severe is an evolutionarily stable strategy for an infectious agent.

An infection that makes its host too ill will keep that host from moving about and make itself less likely to be spread, to say nothing of an infection that tends to kill its host quickly.  Smart parasites (so to speak) keep their hosts alive and sharing for a looong time.  Of course, “smart” here doesn’t say anything about the parasite itself; viruses are only smart in the sense that they achieve their survival and reproduction well, but they didn’t figure out how to be that way—nature just selected for the ones that survived and reproduced most successfully.  It’s almost tautological, but then again, the very universe itself could be tautological from a certain point of view.

It’s an interesting point, to me anyway, to note that today, December 1st, is precisely one week after Thanksgiving.  Of course, New Year’s Day (January 1st, in case you didn’t know) is always exactly 1 week after Christmas.  It’s unusual for Thanksgiving to precede the first of December by a week, because the specific date of Thanksgiving varies from year to year (and, of course, if Thanksgiving were to fall on the 25th of November, December 1st would not be exactly one week later).  It’s an amusing coincidence; there’s no real significance to it, obviously, but I notice such things.

Anyway.

My sister asked me to write something about the vicissitudes of sugar (not her words), and though I don’t mean to finish the topic here today, I guess I’ll get started.  Apologies to those who are waiting for me to finish the neurology post, but that requires a bit more prep and care, and I’m not ready for it quite yet.  Life keeps getting in the way, as life does, which is one of the reasons I think life is overrated.

It’s hard to know where to start with sugar.  Of course, the term itself refers to a somewhat broad class of molecules, all of which contain comparatively short chains of carbon atoms, to which are bonded hydrogen and hydroxyl* moieties.

Most sugars are not so much actual free chains as they are wrapped up in rings.  The main form of sugar used by the human body is glucose, which is a six-membered ring with the rough chemical formula C6H1206.

glucose2

This is the sugar that every cell in the body is keyed to use as one of its easy-access energy sources, the one insulin tells the cells to take up when everything is working properly.  Interestingly enough, of course, though glucose is the “ready-to-use” energy source, it only provides about 4 kilocalories** per gram to the body, as compared to 9 kilocalories per gram for fats.

But the sugar we get in our diets is not, generally speaking, simple glucose.  It tends to be in the form of disaccharides, or sugars made of two combined individual sugars.  Sucrose, or table sugar, is a dimer of glucose and fructose, joined by an oxygen atom.

sucrose

Okay, I’m going to have to pick this up tomorrow.  I’ve gotten distracted and diverted by a conversation a few seats ahead of me.

There are two guys talking to each other at the end of this train car, and they are each seated next to a window on the opposite side of the train, so they’re basically yelling across the aisle to each other.  Their conversation is perfectly civil, and though they’re revealing a certain amount of ignorance about some matters, they are mainly displaying a clear interest in and exposure to interesting topics, from history to geography and so on.

At one point, one of the men started speaking of the pyramids and how remarkable their construction was, and I feared the invocation of ancient aliens…but then he followed up to say that, obviously, there were really smart people in ancient Egypt, just like we have smart people today who design and build airplanes and rockets and the like.  Kudos to him!

These men are not morons by any means.  They clearly respect the intellectual achievements of the past and present, and that’s actually quite heartening, because I think it’s obvious that neither one is extensively college-educated, if at all.

But why do they have their conversation from opposite sides of the train, so that everyone nearby has to hear it?  It’s thrown me off my course.

I’ll close just by saying that yesterday I finished rereading The Chasm and the Collision, and I want to note that I really think it’s a good book, and to encourage anyone who might be interested to read it.  The paperback is going for I think less than five dollars on Amazon, and the Kindle edition is cheaper still.  If you like the Harry Potter books, or the Chronicles of Narnia, or maybe the Percy Jackson books, I think you would probably like CatC.

CatC cover paperback

I’d love to think that there might be parents out there who would read the book to their kids.  Not kids who are too young—there are a few scary places in the story, and some fairly big and potentially scary ideas (but what good fairy tale doesn’t meet that description?).  It’s a fantasy adventure starring three middle-school students, though I’ll say again that, technically, it’s science fiction, but that doesn’t really matter for the experience of the story.

Most of my other stuff is not suitable for young children in any way—certainly not those below teenage years—and Unanimity and some of my short stories are appallingly dark (though I think still enjoyable).  If you’re old enough and brave enough, I certainly can recommend them; I don’t think I’m wrong to be reasonably proud of them.  But The Chasm and the Collision can be enjoyed by pretty much the whole family.  You certainly don’t have to be a kid to like it, or so I believe.

With that, I’ll let you go for now.  I’ll try to pick up more thoroughly and sensibly on the sugar thing tomorrow, with apologies for effectively just teasing it today.  I’m still not at my sharpest from my cold, and the world is distracting.  But I will do my best—which is all I can do, since anything I do is the only thing I could do in any circumstance, certainly once it’s done, and thus is the best I could do.

Please, all of you do your best, individually and collectively, to take care of yourselves and those you love and those who love you, and have a good month of December.

TTFN

*Hydroxyl groups are just (-OH) groups, meaning an oxygen atom and a hydrogen atom bonded together, like a  water molecule that lost one of its hydrogens.  This points back toward the fact that plants make sugar molecules from the raw building blocks of carbon dioxide (a source for the carbon atoms and some of the oxygen) and water (hydrogen and oxygen) using sunlight as their source of power and releasing oxygen as a waste product.  This was among the first environmental pollutants on the Earth—free oxygen—and it had catastrophic and transformative effects on not just the biosphere of the Earth but even on the geology.  The fact that the iron in our mines, for instance, is mainly in the form of rust is largely because of this plant-born presence of free oxygen in the atmosphere.

**A kilocalories is defined as the amount of energy needed to heat a kilogram of water by one degree centigrade.  We often shorten this term just to “calorie”, but that is actually only the amount of heat needed to raise a gram of water one degree centigrade (or 9/5 degrees Fahrenheit).  It’s worth being at least aware of the fact that what we tend to call calories are actually kilocalories.