Tuesday, July 31, 2018

Sporadic spidering this time

kw: blogs, blogging, spider scanning

In the past month or so, amidst ordinary days in which this most modest of blogs gets 30-50 hits daily, a spike in Russian interest pushes that to 100-150 on a particular day, in the space of a few minutes. Clearly a robot or spider at work. This time, there is a series of sporadic spikes over the past few days:

The lesser spikes on the 27th and 30th are mildly interesting, but the past 24 hours is what caught my eye. And as the lower left pane shows, the interest is spread out over posts from the past several years. Now, the "Audience" pane for the past week isn't quite as clear as the one for the past 24 hours:

I had hit the "More" button next to the map on the screen above, and changed the time to the past day. Now we see that, while the rest of the world slouches along as usual (even a hit from Fiji and one from Japan!), someone in the U.S. and someone in Russia each ran a spider that Hoovered up close to 200 pages in a matter of minutes. Probably one of the big spikes is the U.S. one, and the other is the Russian one.

My wife watched as I assembled this post, something she almost never does. She remarked, "Most of that is just people getting a random hit from a search for something else." My thoughts also. I have no idea why my blog, or any other, would periodically get heavy attention from any one entity...let alone two of them.

Finally! Food advice from someone who knows what he is talking about

kw: book reviews, nonfiction, nutrition, medical studies, advice

The apostle Paul wrote to the Colossians, "Why … do you subject yourselves to ordinances: Do not handle, nor taste, nor touch, (Regarding things which are all to perish when consumed) …?" He went on to say that "such things indeed have a reputation of wisdom", but were otherwise without value. He was writing about asceticism, which infected the early church within a matter of months after the resurrection and ascension of Jesus, and to some extent the infection remains to this day.

A similar infection is found in the secular world, with prohibitions about many, many things. In particular, food prohibitions are rampant. Food, as a necessity, comes right behind air and water. For most of us, the time spent obtaining food and groceries, cooking, eating, and cleaning up must add up to at least a couple hours a day. And, wouldn't you know it, everybody seems to have advice about food.

I have no idea how many "weight loss" diets there are, but health.com ranks 38 of them on this page! Then we also find multitudes of shrieking voices from all sides, "Meat is poison!", "Salt kills!", "Eggs are heart-attack pills!", and on and on and on. There must be at least 100 holier-than-thou stances on food that is healthy (or not), moral (or not!), or meets one or another standard of "sustainability".

Let's face it. Humans are omnivores. We can eat anything that was once alive, and a few things that never lived (like salt). Hmm…strike out "that was once alive": raw oysters live a little while in the stomach, as do swallowed goldfish. And come to think of it, when you eat a piece of fruit or other raw vegetable, it is still alive. We can eat anything living or recently dead.

But just to drive the point home: one of our closest evolutionary cousins, the Gorilla, is a strict herbivore. Gorillas are vegans. They eat leaves, and they have very long bowels for their size. They also ruminate, even though they don't have a rumen like a cow or deer or sheep does. I have watched a large male gorilla spend an hour or so eating leaves and stems. Then he brought up a mouthful of "stomach gunk", spat it in his hand and looked at it (I also looked; it looked like greenish feces), then put it back in his mouth and chewed it for a while. After swallowing, he brought up another mouthful and the performance continued, presumably all afternoon. I went on to observe other primates after watching a half hour of rumination. A gorilla has a huge pot belly. They are adapted to eating food with few usable calories, even after rumination, so they have to eat lots and lots of it. By contrast, a wolf or lion has a much shorter bowel. They eat only meat. Meat has many more calories per ounce than a diet of leaves, even leaves of delicious Romaine or Kale (eaten raw). A short gut is sufficient to get most of the caloric value from a meat diet.

Humans, bears, and other omnivores have bowels of middling length. The human small intestine is around 20 feet (6m) long, and the large intestine is about 5 feet (1.5m) long. Though a male gorilla weighs about twice as much as a man, its "small" intestine is 60-70 feet (18-20m) long and its large intestine is also longer than ours, plus larger in diameter. That's what it takes to eat leaves, even the tender, choice leaves the Gorilla selects.

OK, on to the book of the week: The Bad Food Bible: How and Why to Eat Sinfully, by Aaron Carroll, MD, a pediatrician who got into nutrition and education because so many parents asked him how to feed their children. He didn't just look up "received wisdom", but dug into the subject. The more he looked, the more surprised he found himself.

Let's cut to the chase, then backtrack a little. This is the bottom line:
Almost every "Don't eat that!" prohibition is wrong.
Y'got that? Sure, we all know not to eat rat poison, but you know what I really mean, right? At different times in the past, and up until today, we got all kinds of advice:
  • Butter and the fat in red meat cause heart attacks
  • Eating eggs and shrimp raise your cholesterol level
  • Coffee is bad in a whole lot of ways
  • Gluten free is the way to go
  • Diet soda will give you diabetes
  • Don't eat food full of chemicals
  • Organic, ORGANIC, ORGANIC!!!
Do you know what, on that last point, with the exception of salt and traces of other minerals (like the lime in Calcium supplements), everything we eat is organic. We can't digest inorganic stuff. It doesn't have any calories! Of course, the Government has tried to define "organic", as in "organic farming" and "organic produce", etc. Their definitions are contradictory and overblown. Then, that next-to-last point, Chemicals: every material thing is composed entirely of chemicals. You are a bag of chemicals. Artfully arranged, no doubt, but still…chemicals. DNA is a chemical. Proteins are chemicals. Your digestive fluids are chemicals. The taste of an apple or grape is because of the chemicals in them. Glucose, or grape sugar, the only substance your brain can use for fuel, is a chemical.

Oh, you meant we should avoid "artificial" chemicals? Glucose has the chemical formula (CH2O)6. So do several other sugars; they differ from one another because of the way the "H" and "OH" groups hang off the 6-carbon ring that is the backbone of most simple sugars. It is possible (not too hard, really) to make glucose in a laboratory, with test tubes and stuff. Once you crystallize it a time or two to purify it, there is no difference from the stuff made by grapes, or apples, or many other sweet fruits. In your body, many other kinds of sugars and starches (polymerized glucose, mainly) are turned into glucose, and whatever you don't need immediately is converted first to glycogen and stored in the liver, and any excess beyond a certain amount of that, is converted to fat and stored all over the place. Also, excess protein can be turned into glucose or glycogen or fat, depending on the balance of nutrients in the body at the time. And, if you are really low on recent calories, such as after a fast, your digestive apparatus can convert any fat you eat into glucose (and some waste materials). But you have to eat protein to build protein; carbohydrates (including sugar) and fats do not contain nitrogen, which is a part of every link in every protein chain. It is all chemicals, from end to end.

So, is there such a thing as "bad food"? Only in the sense of spoilage! Yeah, if that hunk of leftover roast in the back of the refrigerator is now green and fuzzy, it is probably "bad". If you aren't squeamish, though, you could probably re-fry it and eat it with no ill effects. But what is the "bad food" in The Bad Food Bible? Think things you've been told are "bad for you." Dr. Carroll picked out 11 famously hated foods that turn out to be not all that bad after all.

Along the way, the author discusses at some length just what "medical evidence" truly is. When someone says or writes, "Studies show…", we need to ask, "What kind of study?" He discusses several kinds of things that are called "studies" when people are being sloppy. The story by your Aunt Millicent, about the liniment that a local cobbler makes up, and how "wonderful" it is for her "palpitations" is an anecdote. That's a 50-cent word for "story". If you gather 1,000 stories, is that research? No it is still stories. But someone with an agenda just might call it a "study". To what were the stories compared? How many people tried the cobbler's liniment and never finished the first jar because it just made them feel oily and smell bad?…and it didn't help anyway. Without knowing how often it didn't work, you don't know anything useful about that liniment. At the other end of the scale is the mighty RDBCT, the Randomized, Double-Blinded, Controlled Trial, frequently shortened to RCT. This is called the Gold Standard, for two reasons. Firstly, a properly conducted RCT is truly valuable; it is the only kind of "study" that can determine cause and effect. Every other kind of study can at best hint at, or maybe strongly indicate, an association. For example, it is known that a higher proportion of alcoholics get lung cancer. Does that mean that alcohol can cause lung cancer? No. It was hard enough getting proof that smoking causes lung cancer! Rather, there is a secondary association that provides the link: A high proportion of alcoholics are also smokers. So, the chain of evidence is

  • Smoking → Cancer
  • Factor X → both Smoking and Alcohol Abuse

Whatever "Factor X" is, it must be one of several things that, taken together, make a person more likely to either smoke, abuse alcohol, or both.

The other reason that RCT's are called a Gold Standard is that they are very expensive. Food is one of the biggest industries out there. Food is, quite literally, a trillion-dollar enterprise. So there must be lots of research that has been done on food, using high-quality RCT's, right? No, they are rather rare. Dr. Carroll has to do a lot of digging to find an RCT here or there, and then he must assess the quality. Many try, but few do it well. So most "studies" just don't have the oomph to tell us anything useful.

Where there is gold, there are gold seekers. Among the multitude of paid-for "studies" about food, if you can follow the money you can reason out the conclusion that the researchers were asked to find. That's right. Much "research" was done to "prove" one point or another. Here is the biggest smoking gun: We've heard for 50 (maybe 100?) years that eating too much fat makes us fat, and that saturated fat was the worst. But the early "solution" to saturated fats was margarine, which turned out to be about 40% trans fats, which are much worse for us than saturated fats! Where are the studies that prove that eating fat causes us to get fat? Those that exist are actually poor in quality and there are hardly any RCT's, …and those show little or no association! But a lot of lower-quality "studies" were published, and guess who paid for them? The sugar industry. Now that a few folks with the financial backing to do so have begun conducting RCT's about it, the real culprit is sugar.

Humans lived for tens of thousands of years on high-protein, high-fat, low-sugar diets. Our bodies are used to coping with that. I remember reading an archaeological report about a Roman colony that was abandoned 1,700 years ago or so. The author of that report wrote, "Their teeth were perfect, even the old people. Clearly, they didn't have sugar in their diet." They were also more physically fit than people in colonies of the same era that were closer to the trade routes and could get abundant sugar.

All this is background for Chapter 9: "Diet Soda". Diet soda is well-hated by some. Sugar substitutes (there are 3-4 found different ones in packets on the tables of most restaurants I visit) are all tarred with two brushes, "Causes cancer" and "Promotes diabetes". The fact is, neither is true. All the "studies" on these were done in rats. To speed things up in cancer studies, researchers use strains of rats that are prone to getting cancer. Let's say a study shows that, of rats fed regular stuff, 5% get cancer in one year; of those fed the same food with some sugar substitute added, 7% get cancer. Both these rates are incredibly high compared to human cancer risk for a typical year. But it "justifies" someone saying, "Sweetener X increases the chance of cancer 40%!" (7/5-1 = 0.4 = 40% increase). They never, ever mention that the amount of Sweetener X given to the rats was comparable to you drinking 400 cans of diet cola every day...for a year. I think the rats really died of disgust!

Dr. Carroll's conclusion, after discussing what is really known about sugar substitutes, from Stevia to Sucralose, is that too little is known as yet. However, if there are risks, either of cancer or diabetes, no human trial has been done to figure it out. None ever will be, because you can't pay someone enough to eat a heaping tablespoon of Sucralose (or whatever) every day for a year or more. In concentrated form, it is awful! There is probably an ethics question also. So the follow-on conclusion is that if there are risks they are small, while the risks of excess sugar are very real and much better known. So he lets his kids have a diet soda from time to time. The rest of the time they drink water, except prior to weaning, when they drink milk.

One bit of almost accidental wisdom came from the Federal Government in recent weeks. They proclaimed that it is OK to drink as much as four cups of coffee daily. Wow! I though it was a big deal, a few years ago, when they said, "up to a cup or to, not more." Before that, it was, "The less coffee, the better." But the studies have been done, with enough quality to convince the FDA folks, so they have this new statement.

A final note: Alcohol is a problematic substance. It turns out, a man who drinks 1-2 ounces of the stuff daily, in whatever form, is in the "sweet spot" for living just a tad longer than those who don't drink at all, or those who drink more than that. Women, being proportionately smaller, can have up to one ounce. But for some, that first ounce leads to a second, then a third. So if you are drinking, keep it moderate. If you are drinking less than that, don't increase it. If you aren't drinking at all, don't start. But if you are drinking more, a shorter life will be the price you pay. Of course, maybe that's the life you want, anyway. Just don't drive afterwards, OK? Alcohol and table salt share this characteristic: there is a "sweet spot". With salt it is more dramatic. For most of us, the sweet spot is 4-7 grams daily. Ingesting 3 grams or less is as bad as getting 10 or more. Your body needs the elements in salt (sodium and chlorine) to live. Without any, you die, and soon. So this final point is, as with salt, so with many foods. Too much is probably bad. Too little can also be bad. Find the sweet spot, and you'll be the best off.

Dr. Carroll also hosts the YouTube channel Healthcare Triage.

Wednesday, July 25, 2018

Living without plastics

kw: book reviews, science fiction, near-future, technology, sociology

Look around your house, your schoolroom, your workplace…can you find many objects that do not contain at least a little plastic? Maybe you won't always recognize it. Almost anything that isn't wood, stone, metal, silk or cotton is probably plastic or contains a lot of it. By "plastic" I mean manufactured polymers, from polyethylene to nylon, from Lucite to ABS (bullet proof windows in banks). Even printing ink contains polymers these days. The wires in your computer and phone have plastic insulation.

There are tens of thousands of polymerized materials that are entirely artificial. There are polymers in nature, including all fibrous materials: cotton, silk, linen, etc. Even protein and DNA are aperiodic polymers. But nearly all manufactured polymers have a periodic structure, and are simpler than the natural polymers.

Let us now assume that our plastics begin to disintegrate, turning to goo and then to liquid, one after another. Now what? This scenario is how Drop by Drop, by Morgan Llewelyn, begins.

The idea is a great one. Many SF stories surround troubles with computer equipment or electrical technology either failing or going rogue. But plastic? We are not fully aware how much of modern life depends on them. Actually, in the novel, I was wondering when the author would introduce widespread electrical failure as insulation melted off wires and the generating equipment shorted out. She doesn't go there, and I suppose there was just so much dystopia she was willing to handle.

There is a little tech discussed by characters in the book, but that isn't the author's point. This is her first SF novel, but not her first novel. She has many books in print. Her focus here is on people's reactions to a Change. In the face of overwhelming and irreversible change, some people persevere and even thrive, and some go off the rails. All sorts of reactions are explored as the people in a small town cope (or don't) with The Change, with losing contact with the rest of the world except via a network of ham radio operators who build crystal sets that use no plastics, for example; with the asphalt on roads turning to goo, and then the tires of the autos.

The book is well written, entertaining, and made me wonder, what could bring about such a change, and what would most of us do about it? What if the things that failed weren't made of plastics but of steel?

Sunday, July 22, 2018

A plan to reverse global warming

kw: book reviews, nonfiction, climate change, compendia

The title of the book is Drawdown: The Most Comprehensive Plan Ever Proposed to Reverse Global Warming. It is edited by Paul Hawken, who founded and Executive Director of Project Drawdown. The Project has a large number of affiliated scientists and others who are working on numerous efforts that are at least "carbon neutral" and, it is hoped, able to actually take CO2 back out of the atmosphere. He admits in his introduction that the plan he proposes is the "most comprehensive" because it is the only one. Fair enough. All other plans to date focus on mitigation, on slowing the increase of CO2, and so forth.

It will take some doing for anyone to come up with a "more comprehensive" set of proposals. The book discusses 100, the top 100 from a pool of a few hundred. The top 80 are ranked according to expected reduction in greenhouse gases as "CO2 equivalent"; for instance, methane is something like 30-40 times as effective as CO2 is at trapping heat near the Earth's surface. So reducing a ton of methane is counted as about 40 tons of CO2 equivalent. The other 20 ideas are gathered in a chapter titled "Coming Attractions", rather more speculative possible solutions that haven't been as thoroughly researched.

I was impressed with the scholarship and ingenuity that went into the chapters, including a half dozen essays on related subjects (so there are more than 100 chapters). But I looked for, and didn't find, one critical element. In the discussion of the history of the theory of greenhouse gases in the atmosphere, the early insight on human impact on the atmosphere, in 1831 by Alexander von Humboldt, is dwelt upon, but Svante Arrhenius, who quantified the effect in 1896, is not mentioned. Considering that the discussions of greenhouse effect, climate change, global warming, and a few similar and increasingly politicized terms, are based on mathematical analyses, the utter lack of even a fillip toward math dismayed me.

I remember learning of Arrhenius's work before I was a teenager, nearly 60 years ago. With the mathematical tools available to a ninth grader of the time, it wasn't hard to follow his reasoning, nor to reproduce his results. The tedium comes in adding up the effective ultraviolet/visible-versus-infrared spectra to determine an effective emissivity-temperature relationship for any particular gas. The concept is thus:

  • There are "windows" in the spectrum of a gas, ranges of light wavelength that are transmitted with little or no hindrance.
  • Conversely, there are "doors" in the spectrum, ranges of light wavelength that are absorbed by the gas and heat it up. It then radiates this heat as longer-wavelength infrared (IR).
  • Ultraviolet (UV), visible (V), and near-IR (the shorter IR wavelengths) emitted by the Sun are little hindered by the atmosphere, and strike the ground, heating it.
  • The warmed ground radiates mid- and far-IR (long to very long wavelength IR) upwards.
  • Some of the re-radiated IR passes through "windows" of the various gases in the atmosphere, and so outward into space.
  • Some instead hits one "door" or another, such that it heats the gas, which heats the rest of the atmosphere. Interestingly, nitrogen and oxygen, which make up 96-99% of the atmosphere, depending mainly on humidity, have spectra with very little in the way of "doors".
  • Light that hits a "door" causes heating of the air, which then emits longer-wavelength IR (mostly far-IR) that is radiated in all directions. Simply put, half of it goes back down to increase the heating of the ground, and the other half goes up and out into space.
  • The atmospheric temperature rises until the radiation passing upward through the "windows", and half of that which hit "doors", balances the radiation coming inward from the Sun. At that balancing temperature, total emissivity upward equals total emissivity downward, across all wavelengths.

That is the greenhouse effect. What gases cause the most greenhouse warming, that is, which gases have the biggest and thickest "doors"? Number 1 is water vapor! If Earth had no water at all, being as dry as the Moon, it would be 33°C (59°F) colder than it is (as the Moon is), with an average temperature near -18°C or 0°F. But Earth's atmosphere contains between 1% and 3% water vapor, which causes all this heating.

Although CO2 is much less effective as a greenhouse gas than methane or nitrous oxide, it is much more abundant: a few hundred parts per million (ppm) versus 1.5-2 ppm for methane. The critical thing about CO2 is that we can influence its abundance. We do so by burning stuff. Almost everything we burn for heating and creating energy such as electricity contains carbon. Coal is almost pure carbon; methane has the least, but is still 75% carbon by weight (and 25% hydrogen). But the heating value you get from a ton of methane versus a ton of coal means, kilowatt for kilowatt, it produces only about half the CO2.

Since the year 1800, the amount of CO2 in the atmosphere has risen from about 280 ppm to about 400 ppm. That has caused an average heating of Earth by about half a degree C, or close to 1°F. Note that the same climate scientists who compiled the various IPCC reports on global warming over the past 30 years differ quite a lot over whether it is half a degree, or one degree, or perhaps less than half. "Half a degree" is a sort of average of their opinions.

Here is a point I haven't read anywhere since about 1990: If we go far out on a limb and calculate the effect of CO2 going way, way up, to perhaps 1% (where it affects our breathing reflex), and which is 10,000 ppm, the average temperature of the Earth would rise no more than 4°C (~7°F) above what it was in 1800 AD.

Now, 4 degrees is a large change, and would cause a lot of trouble. But it would not end human life on Earth...just human comfort! Because the #1 issue discussed in Drawdown, the factor that can reduce the greenhouse effect the most, is to eliminate refrigerants containing carbon! No A/C, folks, unless you want to return to using ammonia or CO2 as a refrigerant. Ammonia is actually a great refrigerant, but it is so toxic that even a tiny leak could be catastrophic were it to leak into your house. Effective A/C using ammonia would have to be totally redesigned, to operate outdoors only, in a very well-ventilated area, creating chilled water that would be pumped through the indoor cooling system. More complexity, more cost, and just how rapidly do you think the world's slightly-less-affluent nations are likely to embrace it? CO2 is a less efficient refrigerant, but at least it isn't toxic, though it can cause suffocation, so it still would have to be used in outdoors-only water-loop systems.

Before closing I need to address a typo and an unfamiliar concept. On page xiv in an introductory section, the author is discussing just what a gigaton is. After showing that it is the amount of water in 14,400,000 Olympic-size swimming pools, it is stated, "thirty-six billion gigatons is the amount of carbon dioxide emitted in 2016." The word "billion" needs to be omitted. It is either 36 GT or 36 billion tons, but not both! Secondly, the words "a billion acres" appear a few times, or various amounts such as half a billion or 1.5 billion acres, etc. To help us get our hands around it, one billion acres is about 2.7% of the land area of Earth. Since only a quarter of that land is arable, that comes to about 11% of land that can be farmed.

I like the ideas discussed in Drawdown; it's more practical and well-thought than most other writing I've seen on the subject. I hope the efforts of the Drawdown Project continue. These folks are more level-headed than most of the other loud voices in the climate arena.

Tuesday, July 17, 2018

The little things that keep us going

kw: book reviews, nonfiction, medicine, cellular biology, mitochondria

Did you ever hear of a buccal smear? If you take a teaspoon and gently scrape the inside of your cheek, and put some of the stuff on a microscope slide, that's a buccal smear. The four cells in this photo are cheek epithelial cells, stained with Methylene Blue, from just such a smear.

From the scale bar you can see that the cells are around 50 microns across. They are a little compressed. A typical cell of this sort is a roundish thing about 40 microns in diameter. Methylene Blue stains DNA very well, so each cell's nucleus is seen as an oval blob about 10 microns long.

Today we are interested in something that doesn't show in this photo, the mitochondria, the powerhouses of the cell. Each of the cells above contains around 1,000 mitochondria. Mitochondria vary in size, but here they would be about the size of E. coli bacteria, a micron in diameter and 2-4 microns in length. As it happens, there are a few small bacteria in this photo, the little dots such as the one near the arrowhead labeled "Cytoplasm". Imagine about a thousand of these in each of these cells.

Let's scale this up to a size we can better imagine, and magnify one of these cells by 100,000. Some museums have made models of cells on this scale. Then the cell would appear as a lumpish thing about 4x4x4 meters in size, the size of a big bedroom with a high (12-13 ft) ceiling. The cell's nucleus would be a meter across, not quite spherical. Consider it like a bean bag chair floating somewhere near the middle. The cell isn't just a bag of fluid. "Cytoplasm" is a very complex mix of fluids and organelles. About half of the cell volume is the fluid, called cytosol; "sol" indicates it is a semifluid colloid, not just watery stuff. Just under half of the "solid" material is the mitochondria, and a similar amount of space, or a little less, is taken up by the endoplasmic reticulum (ER to its friends), a highly folded array of membranes that handle protein synthesis. There are other organelles that we won't go into here. Some can be seen in the electron microscope view on the left in the image below.

(This image is © Pearson Education.) The mitochondria scale up to be about the size of a fat sausage, such as a salami, around 10cm in diameter and under half a meter long (say, 4" diameter and a foot long or so). So now you have a bedroom with a bean bag chair suspended in the middle surrounded by salamis, and we'll have to forego describing the "shape" of the ER, except to say that it is a lot like masses of folded blankets. Mitochondria vary in shape also, from nearly spherical to long and even branched. But the sausage shape is common.

So what is this all about? Earlier this year I noticed a rather dramatic shift in my energy level. It wasn't a one-day thing, but I could think back over a few months to "how things were." My usual temperature has been 97.8-98.0°F for many years. It went to 97.6 or less, where it still is. I thought it might be one of several side effects of a diuretic blood pressure pill I had been taking for a few months. If it was, it has been a permanent side effect! I've changed to three different blood pressure medications since then, and the current one seems to have no troubling side effects. But back to energy.

Mitochondria are the powerhouses of the Eukaryotic cell. That's the kind of biological cell that makes up all multicellular life, plus protozoans and fungi, including yeast. "Eukaryotic" is Greek for "Good kernel", referring to the distinct nucleus that contains the DNA. Bacterial cells don't have a nucleus; their DNA is a long, tangled loop attached to one point on the inner cell membrane.

Knowing this, I specifically looked for a book on the subject of mitochondria and their disorders. There was really only one choice in the popular press: Mitochondria and the Future of Medicine: The Key to Understanding Disease, Chronic Illness, Aging, and Life Itself, by Lee Know, ND. Doctor Know is a naturopath, so I was a little leery, but I was cheered by the even tone and lack of hysteria in his writing. He did a great deal of research to prepare the book, which he admits is little more than an outline of many subjects related to mitochondria.

From time to time in the book the author uses a metaphor from popular culture, the Midi-Chlorians of Star Wars. They are actually modeled on mitochondria, but have the added function (in that galaxy far, far away) of tuning certain people in to The Force, so that the Jedi and the Sith have rather magical powers.

The little mitochondria in our cells have almost magical powers themselves. The first part of the book discusses their structure, activities and origins. They almost certainly began as small bacteria that were incorporated into a larger bacterium as a symbiont, on the way to the development of the first Eukaryotic cell. It may be that all cell organelles began as bacterial symbionts, including the nucleus!

Now most of the genes that produce the components of the mitochondria are held in the cell's nucleus, and turned into appropriate proteins in the cell's ER. But a small number of critical bits of DNA are kept within each mitochondrion (5-10 copies per organelle), so that crucial operations can be performed as fast as possible, in seconds or minutes rather than hours or days.

In such a complex arrangement, a lot of things can go wrong. It is amazing that most of the world's people, and plants and animals, live out their lives with little to trouble them except predation. The main reason a wild wolf seldom lives more than seven years, while a pet dog frequently lives twice that long, is that once a wolf reaches middle age, something is going to come along and kill it, frequently a rival wolf. We usually prevent our dogs from killing one another.

But why should a middle-aged wolf slow down? And…why do we slow down? On my Dad's sixtieth birthday, I asked him, "What is it like?" He said, "It is a lot like being 25, except everything takes longer." Now that I am over 70, I agree. Particularly since the beginning of this year. So the second part of the book (of three parts) describes a whole host of things that can go bad as the mitochondria wear out. The section has the cute title, "The Dark Side of The Force".

Section three, equal in size to the other two, around 60pp, describes what we can do about it. The two biggest factors for mitochondrial health? More exercise and less eating, particularly for Americans! The author really believes in Severe Caloric Restriction (though his photos show little sign that he practices it himself). Most things that go wrong with mitochondria trace back to imbalances that lead to excess oxidative free radicals such as superoxide. While there are many products that promote "antioxidants" to mop up such stray molecules, both exercise and a sparse diet (rich in nutrients, but with minimum calories to deliver them) prevent most of the free radicals from forming in the first place. They keep the "electron chain" that mitochondria use to turn ADP into ATP tuned up and running in balance.

One item that is not exactly an antioxidant, but that operates that way among several other things, and that I've heard a lot about recently, is Coenzyme Q10, or CoQ10. It is made in our bodies. But production drops off as we age, after age 30. Some medications, such as statins for cholesterol reduction, hinder its formation, further reducing it, and slowing down our mitochondria. Also, its lack possibly permits them to suffer more rapid decay. The author admits that it is hard to make this stuff into a pill that will work. It is a medium-sized molecule, and is hard to get into solution. So that's something I'll look into. It is only one of a dozen or more nutritive materials he discusses, and among them one more stands out. Magnesium. I am very thankful that this essential mineral (not known to be so essential just a decade or so ago) is added to many supplements including the calcium supplement I use. As usual with a complex machine like the mitochondrion, magnesium does several good things. Without it, several bad things can happen. For example, we think of ATP (Adenosine trophosphate) as a "thing", but this "thing" needs a magnesium ion to shepherd it around. Less magnesium, less energy.

Fortunately, magnesium is easy to get and being a "salty" element it is easily absorbed. A magnesium atom sits at the center of the heme complex in chlorophyll the same way an iron atom sits in the heme complex of hemoglobin, which makes our blood red. The magnesium makes the heme green in plants. The greener the plant, the more magnesium. So eat yer darn greens! (By the way, hemocyanin, the heme complex with a copper atom inside, makes the blood of crabs blue. The "cyanin" part of the word refers to the blue color, not to cyanide).

There you have it. I'll keep a lookout for newer books on the subject. At present, this book stands out, and while it contains a lot of technical language, it is well explained, so the book is easy to read.

Tuesday, July 10, 2018

Even kidneys are political

kw: book reviews, nonfiction, medicine, kidneys, organ transplants, race

A good friend of mine was already on hemodialysis when I first got to know him. We are church friends. His life was quite restricted, not only by the need to visit the dialysis center 3-4 times weekly, but by the severe fatigue that is a side effect of the treatment. When your kidneys are not producing any urine, fluid accumulates. After a couple of days, you've gained a few extra pounds. Those pounds are extracted by the dialysis machine, along with urea and other toxins. But the best of the machines is a poor substitute for a real kidney. It will keep someone alive, but not very healthy. Just the rapid removal of fluid causes severe cramping and headaches.

Fortunately, my friend was able to receive a transplanted kidney a few years later. It made a huge difference in his life! He told me right after the transplant operation that the typical "cadaver kidney" lasts between 10 and 20 years, and then the body begins to reject it, in spite of the best anti-rejection medicines. He was a bit luckier than average; it lasted 19 years. Then he was back on dialysis.

This time, one of his daughters insisted that she be tested to see if she was a "good match", histologically speaking. And she was, a very good match indeed. She donated one of her kidneys, and he is back in comparative good health. Because the match is even better than before, and because of further advances in medical treatment, this kidney is more likely to last him the rest of a good life (he isn't as old as I, but old enough to make plans no more than a few years into the future).

My friend is Asian. I wonder what the outcome would have been if he were Black. After reading Hundreds of Interlaced Fingers: A Kidney Doctor's Search for the Perfect Match, by Vanessa Grubbs, M.D., it seems likely he'd have died by now. The book is partly memoir, partly a medical travelogue, and partly an exposure of a medical system that has not yet become free of racism.

Vanessa and her husband, Robert Phillips, are Black. As a Black woman in medical school, and as a Black, female M.D., she had trouble enough getting the residencies and fellowships she needed for her chosen specialty. Now, part of that may have been that her choices didn't solidify until she had nearly finished medical school. The "solidifier" was Robert. He was already in advanced renal disease when she met him, and being kept alive with hemodialysis.

Love is really blind, it seems. Knowing what she knew (not enough, it seems), she still fell in love with him. She offered him one of her kidneys. After a lot of discussion, and testing that showed how good the match was, he accepted. She had already found out that Blacks on dialysis typically wait an extra 2-4 years, compared to a White or Asian, for a transplant to become available. It is not just a numbers issue. Blacks are seldom put on the transplant list as early as Whites or Asians, and until recently priority on the list was according to time on the list, not time since dialysis became necessary. That has since been changed, but it is not the only inequity in the system.

You'd think, once the transplant was performed, everything would be copacetic. The transplant doctor made a minor error or two, errors of, as Dr. Grubbs puts it, "laziness." Another surgeon, a more diligent one, had to re-install the new kidney so its outlet would not clog! There is much more about issues that a White doctor would probably never notice, but that she did notice.

Along the way, there is a lot of information about kidneys and kidney disease. Dialysis patients seldom talk about their troubles outside their family; I know my friend was pretty quiet about it. But the plain fact is, a dryer-sized machine is, even as we approach the year 2020, a poor substitute for a quarter-pound organ. And it all comes down to glomeruli.

The title of the book describes an image like this one, a highly magnified portion of a glomerulus. The glomeruli (plural of glomerulus) are tiny, highly-structured tangles of blood capillaries situated each in its own capsule. The capillaries have some special features that make them efficient filters, to remove the right amount of fluid and toxins from the body. The toxin-laden fluid collects in the capsules. Tubes from all the capsules are gathered together to feed the ureters that send urine to the bladder.

A glomerulus is small. There are about four of them in each cubic millimeter (a pinhead) of inner kidney tissue; about 4,000 per cc. This comes to 2/3 of a million per kidney. And they aren't just passive filters. They contain enzymes and other active "machinery" that cooperate in blood filtration. It has been said that the kidney is second only to the brain in complexity.

Because of this complexity, it will probably be a good, long while before researchers figure out how to grow someone a new kidney from their own stem cells, making auto-transplanting a reality and eventually closing down most dialysis centers. It is one thing to grow someone a new ear or fingertip (we're nearly there right now); but even growing a liver would be easier.

I hope, long before auto-transplantation is developed, that the remaining racial disparities are dealt with. In addition to race, there is money. I'll let a quote from the book suffice:
"We get paid much more to keep someone on dialysis than to keep them off it…It's profitable to build another dialysis center, but we haven't figured out how to build comprehensive palliative care services."
The fact is, not everyone in end-stage renal disease should have dialysis. Until the kidneys totally fail, certain palliative care and other measures can afford a person a better quality of life. And even at the very end, some people have the fortitude to decide, "I've had enough of this. Uremia isn't the worst way to die; better than most. It's time to go." Very few doctors, who got into the business to "help people", usually internalized as "help people not die", are willing to offer a terminal patient every option, rather than just the options of "fighting the disease."

I am not sure how effective an activist Dr. Grubbs is, but the presence of this amazing book is a great first step to exposing some issues that have been swept under the rug.

Saturday, July 07, 2018

The ChRIstMas sEason

kw: book reviews, crime fiction, short stories, anthologies, christmas

It seems there is a book series for everything. For those who like to read a lot of crime fiction, I find the Soho Crime Series. The volume that caught my eye is titled The Usual Santas (no editor[s] named), and the title is that of a story within by Mick Herron.

The title story is perhaps the most memorable. Eight mall Santas have finished their service for the night, and gather together as is their wont for a bit of complimentary grub before going home. Also, as is their habit, they do not change out of their Santa costumes, preferring to not know who their compatriots are, though they have met this way, season after season, for many years. But they find a ninth Santa among them. They discuss how to determine who the "newcomer" might be. You didn't think I would tell you more than that, did you?

The eighteen stories are in three sets, lighthearted, dark, and warmhearted (each in its own twisted way). They are set all over the world, in all imaginable cultures among those that have adopted, at least in a mercantile way, the Christmas season. A Hindu street urchin with a flair for drawing ponders how to depict her close friend. POW's in North Korea (set in 1953) try to cobble together some kind of seasonal cheer. Jane Austen ponders the loss of a dowager's diamond necklace. As one might imagine, one fellow's mischief is another's mayhem.

Fun stories to read. I seldom read crime, but a collection of this quality, I'll make an exception for.

Monday, July 02, 2018

A searcher's story

kw: book reviews, nonfiction, spirituality, faith, memoirs

I was tempted to title this post, "Looking for God in all the wrong places," but it seems a bit too cheeky, don't you think? Alan Lightman has been a prominent physicist, and is that rare breed, a scientist who is also a qualified professor of the Humanities. It may in part stem from an experience he had in his younger years, as related in Searching for Stars on an Island in Maine: lying back in a small boat near his favorite island, looking into the starry sky, he had a transcendent experience. You can't un-experience such an experience.

Make no mistake, Dr. Lightman is a committed scientist. He is thus most comfortable with a Materialist philosophy, which posits that the physical world is all there is. As one of many paraphrases puts it, "If you can't measure it, it doesn't exist." And we must admit that scientific materialism has gotten us pretty far. But, while he is "most comfortable" in Materialism, he isn't entirely comfortable with it or within it. There is that pesky experience—and there have been others—that is just as real to him as the shoes on his feet.

Science and Religion represent the stereotypes of Relativism versus Absolutism. Although there are certain absolutes in the scientific realm, and some relatives in the religious or spiritual realm, the dichotomy is pretty clear for most instances. As a committed Materialist who nonetheless finds in himself a yearning for something Absolute, Dr. Lightman dwells in a boundary land.

It is sometimes said that scientific evidence must include reproducibility. If I mix chemicals A and B and chemical C is always produced, I can try to publish the results of my experiments. But the journals (major ones, at least) will send the article to other scientists to review, to pass judgment, whether it is worth publishing. If the experiment can be replicated, of course, at least one reviewer is likely to do just that, to make certain that chemical C does indeed result, and not chemical D or E…or nothing at all. Of course, all the experiments that are that easy have been done and published long ago, so now a reviewer will instead determine if the experiment is at least repeatable in principle. Only in the most controversial cases will someone attempt to replicate the experiment.

I like to pose the following to my scientific friends:
Non-repeatable phenomena: Many people engage in a certain activity that is known to usually evoke certain emotional responses in other people. This activity can be carried out by one person alone, or several persons carrying it out together. A large number of standard "recipes" exist (though we are not talking about cooking here). Frequently, following a specific recipe yields a known result. But not always. Some people try, but get a different result, sometimes even a response opposite to that expected. The outcome is not at all consistent!
Can you think what this activity may be?

Singing. And before you think, "Oh, some people just don't have a good voice," I am sure you know of people with a fine, melodious voice who nonetheless cannot convey the expected emotional impact of a specific song. Even: not all expert, operatic tenors can sing "Nessun Dorma" and get the same response that Luciano Pavarotti could. And I suspect that nobody with a "good" voice can effectively convey the power of a Bob Dylan song.

But what about simple systems? One of the simplest systems of all is a single electron moving through a hole and hitting a detector that can tell you where it hit (a sensitive CCD can do that). It may not be simple to set up, but once operating, suppose that roughly one electron per second is released to zoom through that hole. You are in a room with many others, and a screen is set up to record the results of each electron's impact on the CCD. You are given the chance to place a bet on where the next electron will hit. Do you place a bet?

If you know the initial speed and trajectory of the electron, and the diameter of the hole, you can calculate with absolute certainty, using the law of diffraction, what is the probability that it will fall on any particular segment of the CCD. But nobody can predict on which segment the next electron will land. So here in one experiment you have an Absolute matter and a Relative matter.

The book's chapters do not dwell on electrons, but are instead titled things like "Hummingbird", "Truth", "Transcendence", "Monk" and "Death". The second chapter is titled, "Longing for Absolutes in a Relative World," and introduces the rest. I kept hoping to read that this seeker after faith had found faith in God. At least in this book, he has not done so. An absolute God is apparently a step too far for him, an Absolute just too, well, absolute. But when you have experienced transcendence, you can never forget that there are things our relativistic science can never account for, and perhaps, the things that it can account for are in the minority.