Tuesday, September 30, 2008

Until gender doesn't matter

kw: book reviews, nonfiction, gender issues

It never failed. Twice I've shared an office with a woman, and every time a man came in who didn't know us, he'd either address me as though I were the only one there, or address her as though she were the secretary. The fact is, in both cases we were equal colleagues. With my colleagues' agreement, whenever I thought we'd get away with it (and that was usually), I'd interrupt by saying, "Excuse me, that's my boss..." Wish I'd had a camera handy!

Of course, I've been in on a couple of bull sessions with the subject, "If all the bosses were women." The usual conclusions were, one, war would probably end because by the time a man is a commanding officer he knows better than to go up against a woman, and two, men would likely become little more than pets. That last recalls Garrison Keillor's witty riff on Lake Wobegon, "where all the women are strong, all the men are good looking...". I've lived in the frozen north, where there were plenty of the "Norwegian bachelor farmers" that Keillor lampoons weekly. I know a story or two that substantiate their fear that, should one of them marry one of those strong women, he'd soon be sidelined. One of my neighbors remarked about another, "Yeah, she bought him a big truck and these big gloves so he can drive around and feel important. Really, she just keeps him for a pet."

What would really happen if women ran things? Dee Dee Myers, former Press Secretary for President Clinton, takes a whack at the issue in Why Women Should Rule the World. Like any good debater, she takes her theme in three parts: "Why women don't rule the world", "Why women should rule the world", and "How women can rule the world" (italics are mine).

The historical reason for "Why not?" is, under subsistence conditions women are too valuable as childcare providers. Since a large segment of the human race got more prosperous, however, the reasons are, it is just a habit, and the old "Men are stronger so just try to stop us anyway" gambit. The old Greek play Lysistrata has one answer to the last: "If you don't, I won't!" (of course it was written by a man, Aristophanes, expressing the castration phobia in a new form).

Where women do have some authority, Myers shows that things do indeed work out differently. We have to drop the PC "everyone is the same" crap and understand: woman and men are good at different things. One salient fact shows why: The major corporations which have significant female executive leadership, including female CEO's, rank at the top in profitability and growth. It indicates that the things women are better at are as necessary as the converse. In a sense, denying women leadership roles puts a company, or a society, at a disadvantage. As Geraldine Ferraro put it, women in power "raise issues that others [i.e. men] overlook, pass bills that others oppose, invest in projects that others dismiss, and seek to end abuses that others ignore" (quoted on p.93).

Things are changing regardless. According to an article Myers cites (Journal of Accountancy, April 2004, by Maureen Duffy), in another year or two women will control half the wealth of the U.S., some $22 Trillion (the figure given in the book is grossly in error; this is from the article itself).

The last chapter points the way. In each kind of enterprise, there is a sort of Critical Mass (and I don't mean a room full of complainers!). For example, the board of directors of many corporations with at least three women simply run differently than those with two or fewer. For running the country, the critical mass is likely to be one: whenever a woman gets elected President, things will be Different. I know, inertia is hard to overcome, but just giving a battleship a big nudge in a different direction will make a big difference in its final goal. The recent candidacy of Hilary Clinton is already one such nudge. Like her or not, she has made a difference.

The author thinks it likely that "...if we eliminate the conflict between having a high-powered job and having a family, unravel the mysteries of innate aptitude and interest, and root out discrimination, there will still be more women in social psychology and more men in engineering? And isn't that okay?" The key issue is not to drive women either to or from social sciences or "hard" sciences, but to allow those with aptitude to pursue what they are good at. Period.

So if your little girl wants to play with guns and trucks—most don't, but a few do—let her; if your little boy wants to play house more than play war—most don't, but a few do—let him. And right up through the scale. Even more, if your grown-up girl that once played house and dollies wants to run the country, don't stand in her way. It makes me wonder how Margaret Thatcher might deal with Iran's Mahmoud Ahmadinejad. The Iron Lady would not likely flood him with crumpets and tea, but just might be able to get through his armor nonetheless. Lord knows no man has yet done so.

In the end, Ms Myers is not arguing for 100% female authority, but proportional rule. Half the people are women, so half the leaders ought also to be women.

Monday, September 29, 2008

A friend in his need

kw: musings, prisoners

I had occasion recently to visit a state prison for the first time. I won't write much about the acquaintance whom I visited, so as not to expose him unnecessarily. Rather, I was struck by the process and the environment.

One must first make an appointment a week in advance, and leave contact numbers in case the prisoner denies the visit. The day of the visit, I figured I'd need a half day for this 45-minute visit, and that was about right.

One must arrive at least half an hour early. I almost didn't get in; I was just "under the wire," and the fellow right behind me was denied entry. Had he got in, there would have been three men visiting that day and time. As it was, there was only one other man and the rest of the visitors were women. The other man was with a woman his age, and I surmised that this was a couple visiting their son. What a sad duty! The rest of the visitors were mothers, wives, girlfriends, and just a few little children with their mothers, visiting a father.

One is allowed at most three things upon one's person: one key to the car, a picture ID (but not the wallet you usually keep it in), and a money order if you are making a gift. No material gifts (no cake with a file in it, for example) are allowed. I found out later from my acquaintance that, just to send him a pair of reading glasses, one must mail them to the prison hospital, and they will deliver them, and a book must be sent postmarked from the bookstore from where it was bought; no personal return addresses.

After being checked in and getting a visitor's badge, one endures a half hour of waiting to be let in. The group had to pass through several electric gates. There is a two-gate "airlock" just to get out of the building, then two more gates, each of which passes through a high fence topped with razor wire, and a final "airlock" into the building where the meetings occur.

There are two meeting rooms. One for "white badges" and one for "red badges". I had a red badge, because I was visiting a medium-security inmate. There is no visitation for those under higher security. Eight people in five groups went in and sat on the outside of a thick, cinder block half-wall. A few minutes later five inmates entered, and each found his visitor(s) and sat across from them. A handshake or hug over the wall is permitted, but then everyone must sit.

I found out the inmates have quite a process to pass through also. No matter when their appointment will be, all are gathered at Noon. I had waited half an hour; he had waited more than two hours in a room without chairs for this visit. He suggested next time I try to get a 12:30 appointment! Fortunately, he was in only for a short stay (this time) and was returned to his "on parole" status a week later...but I'll remember, 12:30 if I visit anyone else there.

I have called him "an acquaintance" because I'd only met him twice before I learned that he'd committed a minor parole violation and been re-incarcerated. He'd already served 16 years, and been out about a year. He's really happy someone visited him, so I suppose we'll become friends.

I suppose I've led a sheltered life. This is the first person I've known who has done hard time in a state prison. Should I be concerned? My father thinks so. In an uncertain world, all I know is that it is best to trust in God. I cannot live in paranoia, though a prudent caution is warranted.

Thursday, September 25, 2008

Of the past and the ghosts it leaves in us

kw: book reviews, nonfiction, essays, memoirs

The ad for Sightline Books in an endpaper calls the genre "Literary Nonfiction". Family Bible by Melissa Delbridge is a book of essays, each a mini-memoir, a handful of stories of various periods of her life in Tuscaloosa, Alabama.

Her opening lines made me wonder what I was getting myself in for: "My relatives don't take travel lightly. Hell, a few of them pray before making a long-distance phone call." And a little further along I began to get apprehensive: "Swimming and sex seemed a lot alike to me when I was growing up...", where she explains the similarities, the doffing of clothing, the liquids and unguents involved. Well! Fortunately she confined a deeper examination of the subject to one of the essays, and pretty much skated over the details even then. Her interest is clearly people's attitudes more than their actions.

There's plenty of action, however...this is how attitudes become known. Her father's wild ways and ultra-charming way of mollifying her mother; her mother, finally unmollified, taking the kids to the other end of town (For a family that didn't travel, that was far enough). Her classmates, some well-behaved, most not; the mental patients she cared for at two hospitals; the 'broken ones' and 'turned-in girls' she knew, whether incarcerated or not. All in all, she finds that most folks end up broken in some way or another. We all struggle to survive with whatever we've got.

For these are stories of survival. Most of the ghosts in her memory survived, though a few didn't. The deep South has a reputation for more violence, incest, and general Hell-raising than the supposedly more genteel North. In my estimation, the sins are as numerous and as deep in both places, just expressed in different ways. But she has a point, that a couple of her cousins can chill you to the bone just by shaking your hand, or with the look you get when they say, "Hello." That anything taken to excess creates evil, whether alcohol or religion, and that everyone has an excess of their own. Everyone.

Tuesday, September 23, 2008

How Apollo's arrow misses

kw: book reviews, nonfiction, mathematics, modeling, philosophy

There is a simple, repetitive calculation called a Shift Map, based on kneading dough, that illustrates the problems caused by repeated calculations that lose precision as rounding errors accumulate. While we knead dough by repeatedly folding and stretching, in this model, the lump is stretched to twice its length, cut in half and the two halves set atop one another before the next stretch. Now imagine two points in the lump, say two yeast cells, that were once close to one another. With each cycle, they get twice as far apart, until one of them is moved beyond the cut point. At the next cycle, it starts somewhere near the opposite end, then begins to move across again. From that point, the distance between the two cells is not a simple doubling of distance any more. Also after the first time it crosses the cut, there is no simple way to calculate where the cell will be after N cycles.

The mathematical model of this situation is very simple. The position of a cell can be denoted x, and its position after the next cut is then xn+1 = 2xn mod 1. The mod function divides and leaves a remainder; in this case it removes any portion larger than 1, so 1.1938 becomes 0.1938. A cell beginning at 0.34 moves to positions, 0.68, 0.36 (1 was removed), 0.72, 0.44, 0.88, 0.76, and so forth.

In a continuous system, most positions for a cell never return to a former position, and the cell's motion soon becomes unpredictable from first principles. However, when we model this action with a computer, the whole system becomes totally predictable! The reason is the finite size of a "number" inside a computer, and the fact that only rational numbers can be computed. As a matter of fact, not all rational numbers can be stored accurately in computer memory, only those that represent a finite sum of powers of 1/2. For example, any multiple of 1/3 is stored in binary form as 0.010101010101… and so forth, but eventually you have to stop. So what is stored is not exactly one-third. In fact, 1/10 is also stored as a repeating binary decimal and cannot be exactly represented in binary form!

In most computers, a "word" is a 64-bit quantity. 8 bits are used to store an exponent, two bits for the number's sign and the exponent's sign, and the remaining 54 bits are used for a normalized binary value. Thus 1/3 is not actually stored as 0.01010101 and so forth, but as
I put pipe signs (|) between the sections to emphasize their use. The first 01 means "positive number, negative exponent", the 00000001 is the exponent 1 (so because it is negative, it means "divide by two"), and the rest of the alternating 1's and 0's store the value 2/3, as accurately as 54 bits allows. The whole thing means 1/3, with a minor error after the 54th binary digit. That is the 16th decimal digit.

What happens, then, when we run this through the dough-stretch-and-cut routine? Doubling the number above is accomplished first by removing the negative exponent. So the first ten bits are now 00|00000000, and the whole thing means 2/3. Double it again, and the number stored begins 00|00000001, and the whole thing means 4/3. But we have to subtract one from this to get the remainder for the mod function. The "add" unit in the computer does this by lining up the internal number for -1.0, which is 10|00000001|1000000 and a whole lot more zeroes, with 00|00000001|10101010 and a whole lot more alternating ones and zeroes., then subtracting the value sections from each other (you don't subtract the exponents, but the unit does determine the final sign by checking which sign is negative).

The result is 00|00000001|001010101010 and a lot more alternating ones and zeroes, but notice that the start of the value section is two zeroes. This is "normalized" by shifting two positions to the left, and subtracting two from the exponent. It has been a 1, so now it is -1. And the resulting number becomes 01|00000001|101010 and so forth. This is just 1/3, however, the next-to-last binary digit is no longer a one but a zero. Precision has been lost.

This kind of lost precision continues to occur with each cycle. Rather than spend a lot more words, let's look at the first fifteen cycles as shown in Excel:

Binary rounding errors don't become visible as decimal rounding errors until the sixth cycle, but they compound thereafter. The number is stored with 54-bit precision, so we ought to expect it to take 54 cycles to exhaust the bits…and that is what we find!

The value at the 52d cycle, 0.625, is stored as 00|00000001|1010000000 and more zeroes. 0.25 has just one "useful" bit in the value section, as does 0.5, and the next doubling produced 1.0, which the mod function returned as zero. From that point, it is zero all the way. The model has totally succumbed to rounding error. A final bit before going on: you can look at the value section of the initial number and tell the total history for the next 54 cycles. For most starting values, after 54 cycles you'll get a zero! If you use a number like a trillionth or so, it'll take longer, but no matter what, this calculation is destined to reach zero in a relatively small number of iterations (a couple hundred or fewer). Finally, you don't gain much by using a longer computer "word" to store a number. Suppose the value section had 120 bits rather than 54. Nice idea. But it would "go to zero" after 100 iterations (or at most, 200). Small help that.

OK, all this is background for The Future of Everything: The Science of Prediction by David Orrell, PhD. Dr. Orrell is currently a controversial figure for his assertion that the forecasting of weather, economics, and public health are not a result primarily of mathematical chaos, such as the "butterfly effect", but of model error. The simple system modeled above is one example of model error making a model useless for long-term calculations. Although chaos effects make the path of the yeast cell hard to predict after several cycles, we can run the model to do so. But once it all "goes to zero", prediction is over.

Complex systems have more than one equation, and the equations are larger. A weather prediction model, such as the Global Circulation Models used by NCAR and others, may have millions of geometric elements, and a few dozen equations representing the state of the modeled weather in each element, that must be balanced across all those millions of elements. The starting point is the values of the equations for each element at some point of time. It may take hundreds of cycles to model the weather for one day, and several thousand for a ten-day forecast.

Fortunately, the kind of rounding errors I emphasized in the Shift Map model tend to compensate for one another, otherwise no model could run for more than a hundred steps or so. But there are other kinds of error. The most significant is sampling error: the "weather" in most of those millions of elements must be estimated from readings taken at a few tens of thousands of locations around the planet. Our coverage over the oceans is particularly spotty.

Also, the equations used are mostly empirical approximations of what an air mass the size of New York City, and a km or so deep, will do given the temperature, pressure, wind motion and cloud cover of all its neighboring elements, plus its own. Orrell likens these approximations to epicycles, those little circles used before Kepler to "correct" the motions of the planets and make predictions of eclipses and other syzygies. Epicycles worked well, but on p.41 the author states,
"The fact that it worked quite well as a model of the universe is a poignant reminder that a model that can be made to fit the data isn't necessarily an accurate representation of reality."
The map isn't the landscape, and the model isn't the system modeled. There is lots of room for the unexpected.

Weather isn't the only complex system that people tackle with mathematical models. The economy is a big one, but is considered less complex. For example, there are less than 300 nations, and a much smaller number of stock and commodity markets, so macroeconomic models don't have millions of "elements" to work with, just a few hundred simulated national markets. These markets are based on the "average man", which is considered a soulless bag of reactions to stimuli such as unemployment figures and corporate profit announcements. But once you realize that the behavior of a few million "average men" must be empirically modeled by some statistical beast, you find epicycles again. Both weather/climate and economic models use Ordinary Differential Equations (ODEs) in abundance as the foundation of their modeled structures. These may not be the best in all cases, but "they can be solved using mathematics" (p.115).

The trouble with both is, there are too many parameters that we don't know very well. I once knew a meteorologist (now deceased) who was brought to a campus to add the simulation of lightning to a model of thunderstorms. I asked him about it, and he said, "We don't know where, exactly, a new stroke will start. We have areas of greater likelihood, and have to pick a random spot in one of them." With some tuning, the model was a pretty good simulation of thunderstorm dynamics. But the point was that it was overdetermined: you could get it to simulate a lot of very unrealistic thunderstorms also. About this phenomenon, the Dr. Orrell writes,
"The models suffer from the same problem [that] the Greek Circle Model did: they are too flexible. As Will Keepin put it, modelers can pull the levers and make the model do whatever they want…It is the signature of uncomputability." (p.205)
Ah, uncomputability. It is his term for a phenomenon that cannot—and maybe never can—be simulated from first principles. This is not because of mathematical chaos. It is because, like Conway's game of Life (a seemingly simple cellular automaton with complex behavior), most of what happens is emergent behavior, not strictly implied in the "rules of the game."

One method used by modelers, particularly weather modelers, is to run an ensemble: to run several simulations with slightly different starting conditions, or to use a number of programs that run in slightly different ways or with different size elements. But they are all based on a similar set of simplifications. The author writes,
"[An] ensemble of wrong models does not make a right model, and the spread between the results is not an accurate measure of uncertainty." (p.301)
This is because of something Don Rumsfeld is famous for calling "unknown unknowns". There are things you know you don't know well enough, the "known unknowns". The real stinkers are the things you don't know at all, the things you don't know you don't know. Considering that, in the metabolism of a yeast cell too small to see, there are parameters we know at best only within a factor of ten, and other parameters we've never thought of, it is no surprise we don't have good models of the dynamics of cellular metabolism.

We need to be a little humble. There are things we can't hope to know well enough to simulate them. It would take a computer bigger than the weather to simulate the weather with any accuracy, assuming we got all the parameters and starting values right in the first place. There are billions of people whose emotional state and level of blood caffeine determine the motion of stock markets. And evolution is going on all the time as bacteria and viruses that don't even know we are there strive to make a living that just might come at our expense. Bohr said it best: "Prediction is hard, especially about the future".

Monday, September 22, 2008

Fat conversions

kw: musings, obesity

I've been in calorie-watching mode for a few months. Losing the first twenty pounds was relatively easy because stopping my cholesterol medicine reduced my appetite; that stuff had made me always ravenous! I'd like to lose another ten pounds, and get by BMI closer to 27; it is 29 now, which is too close to the threshold of 30 for obesity.

Lately it got me thinking about the numbers. I've heard for years that each pound of body fat represents 3,500 Kcal (to use the Physics unit). Also, it is published everywhere that a gram of fat that you eat contains 9 Kcal. Now, a pound weighs 453.56 grams; 453.56 x 9 = 4,082 and some change. 3,500/4,082 = 0.86. That implies that about 86% of a fat cell is stored fat. Fat cells must contain a little protein also, but perhaps not much. I just had to dig into it.

This annotated image of fat cells is found with many other histology illustrations at this UCLA med. school web site. Cell membranes, shown in pink, are also fatty. The nuclei are more purplish (also the rare blood vessel or two). There is clearly very little protein to contend with. Adipose cells are primarily tanks containing stored fat.

It appears that the stored fat makes up more than 90% of the volume here. The difference between the storage percent and the 86% I obtained above must represent some very small conversion losses. Now I understand why so many nutrition writers say that the fats we eat are efficiently converted to body fat!

It also underscores, for me, that if I really want to reduce my weight another ten pounds, I have to eat 35,000 fewer calories than my metabolism needs. There's no way around the math.

Thursday, September 18, 2008

Fogged in

kw: musings, reading, measurements

In the former post I closed with the statement that Minders of Make-Believe is well written, just rather dense with facts. I am not satisfied with that statement. Reading other books goes smoother. I remembered noticing that the pages looked "more packed." So I did some measurements, including a Fog Index.

The Gunning Fog Index is a statistical measure of how hard it is to read a piece of text. One gathers three numbers and calculates from them a number that estimates the level of education needed to read the text. The three things are
  • W = The number of words in the selection; this should be at least 100.
  • S = The number of sentences.
  • C = The number of "complex words", meaning words of three syllables other than those formed by adding -er or -ing to two-syllable words.

These are combined according to this formula:
F = 0.4*((W/S)+100*(C/W))
This means, the average words per sentence plus the percent of complex words, all multiplied by 0.4. If the result is 12, one needs to graduate from high school to easily read the text. Few commercial publications have Fog Indices greater than 10. "Reader's Digest" scores a 9.

I tested Minders and a book I am currently reading which I'll here call simply Future, by analyzing a full page of each.

For Minders, W = 423, S = 14, and C = 48. W/S = 31.4 and 100*C/W = 11.4. This yields F = 17. Seventeen! That implies at least a Master's Degree!! The market for such a book is restricted indeed.

For Future, W = 349, S = 16, and C = 39. W/S = 22.8 and 100*C/W = 11.1. This yields F = 13.5. That implies a college sophomore. The market is much larger, but is still a small fraction of the U.S. populace.

The type face of the two books is the same, but Minders has tighter leading ("ledding"), the spacing between lines, so it has 37 lines per page, while Future has 31 lines per similarly-sized page. Both the word count and the line count indicate that the former book has 1.2 times as many words per page. They have nearly identical words per line of type. Since they both have about 350 pages, the one book is equivalent to a 420-page book, compared to the other.

Now, I have a 17-year or greater education (two years beyond my MS), but I found Minders hard to read for extended periods. It is interesting, but it simply requires a lot of work. So I revise my statement: Minders is well-written...for an ordinary soul with a PhD in history.

P.S. The Fog Index of this post is 9.6.

Tuesday, September 16, 2008

The new age of innocense

kw: book reviews, nonfiction, books for children, history

I tried and I tried, but when I saw that in a week of reading I hadn't made it more than one-third of the way through the book, I threw in the towel. I sadly have to declare that it is a reference work disguised as a popular historical survey. The book is Minders of Make-Believe: Idealists, Entrepreneurs, and the Shaping of American Children's Literature by Leonard S. Marcus.

Books written specially for children, other than texts, have a history in America dating almost from the landing of the Mayflower. The key idea I gleaned from the opening chapters and a skimming of the last chapter is that, of course, the writers, editors, publishers, and booksellers are all adults who produce books for one of two markets: firstly, the adults who buy books for the children they care about; and secondly, those children who can be reached by mass advertising, and whose families are sufficiently prosperous, that the children will nag parents and other familial adults to buy them the book.

There is a third market, libraries, which buy books the librarians think will appeal to children (Modern libraries' circulation records give them instant feedback how they're doing). With nearly 3,000 new titles published yearly, competition is now intense.

While the author traces primarily the trend in book publishing, there is a fascinating development of public libraries and their increasing focus on their children's sections.

Throughout American history, children's books have been written to be entertaining to the greatest extent the adult public is comfortable with, and with the minimum of "wholesome instruction" they can get away with. In Puritan America, the former was nearly absent and the latter paramount. Nowadays, wholly magical entertainments are the rule, which have no discernible pedagogical intent.

Considering what my son preferred to read while growing up, I see—once he was able to read textual books rather than "picture books"—three trends:
  1. Adventure series such as the new Hardy Boys books (not the older ones). He cared much less about Tom Swift, upon which I'd doted. I am bemused that the Hardys could solve some three hundred mysteries during a single year in which one was 17 and the other 18.
  2. Comic collections, primarily Garfield, Foxtrot, and Calvin.
  3. Magical epics such as the Redwall and Harry Potter books—two very different occupants of a similar landscape. More recently, the Xanth and Star Trek series (the latter being semi-magical in my view). He totally eschews nonfiction: "I get enough of that in my textbooks."
Had he been a dreamier child, I'd have been more concerned about his connection to reality than I am. He knows magical reality when he sees it, and wasn't influenced to think he could get away in the real world with the shenanigans his storybook heroes accomplished. So I see the largest trend in the subject of children's books over the past four hundred years is the gradual disspation of adult fears, though a large part of this in recent decades has been an increasing self-absorption among those adults. Most of 'em aren't paying attention any more.

Back to Minders: It is well-written. I simply succumbed to a flood of facts. I'll pace myself as I read the rest of it in tandem with other books that I can zip through with more of a sense of escape or engrossment.

Monday, September 15, 2008

Making that picture perfect . . . in size

kw: methods, instruction, image optimization

This tip is too good to pass up. There is a little, unobtrusive icon in the Picture toolbar in the Microsoft Office products, which I only noticed recently. Though I've been using Office 2003 for five years, it simply escaped my notice. When your mouse cursor hovers over the icon I have highlighted here (the tenth), a hint pops up: "Compress Pictures".

In the past, based on advice I received a decade ago or more, I'd pre-optimize all the images I was going to use in a PowerPoint or Word document by changing to a resolution consistent with the final purpose (print or projection) and using either GIF or JPG compression to minimize the number of bits needed to store the image once it was embedded.

As a side note for those who need it: GIF uses run length encoding, so it is best for images such as screen shots or graphics such as those produced by Visio or a CAD program. JPG uses fourier series optimization, which drops out more detail as you use a smaller "quality" criterion. A "quality=90%" JPG looks as good as either a GIF image or an uncompressed (BMP, for example) image. However, for most screen shots the GIF version will be smaller, while for most photographs the JPG will be smaller.

The screen shot above is 416x63 pixels, which would take about 26 Kbytes to store as an 8-bit BMP file and three times that much for a 24-bit BMP. As a JPG file it is 10 Kbytes, and as a GIF (which I use here) it is 7 Kbytes. The GIF file for the image below has even better compression, because there is less detail: an 8-bit BMP would require 145 Kbytes, but the GIF size is 11 Kbytes.

I couldn't resist trying out the idea with a slide show I was planning. I started with images from my digital camera, some cropped. The uncropped ones were 1.5 Mbytes in size, and at 3000x2000 pixels, much too large for projection or printing once embedded in PPT slides. Even the smallest crops were close to a Mbyte each. The final file size was 27 Mbytes, yet it has only 25 slides! I first made a print version. Clicking on the Compress Pictures icon yielded this dialog box:

The default setting is for Print resolution. I changed only the first item, selecting "All pictures in document", and left the resolution at Print (200 dpi). I saved the result with a modified file name.

An image that sits nicely into a titled PPT slide is about 4x6 inches (around 10x15 cm), so at 200 dpi such a picture would need only 800x1200 pixels. That alone reduces the number of pixels by a factor of 6.25. The resulting file's size is 4.5 Mbytes, about 1/6th the size of the original file.

Then I redid the compression using Web/Screen resolution, which is 96 dpi. The number of pixels to be stored is now 1/27th of the original. Saving with yet another file name, I saw that the file size is now 1.3 Mbytes. This file, when projected, looks as good as the Print-resolution version (and the orignal), though there is a difference visible when pages from the two files are printed.

Next I tried this method with a large Word file I've recently been asked to edit at work. It is humongous: 100 Mbytes, yet is only 54 pages, and has 57 screen shots. Looking at them, I could see that they were pasted in, and had probably not been saved first as a file or otherwise optimized. They are mostly 1024x768, 24-bit screen shots. I tried Compress Pictures, and Print resolution (the document is intended for printed use). Guess what? No help whatever. The new file was just as large as before!

I tried another method I'd heard of for finding out which images in a Word file are too large. I saved it as HTML. Amazingly, all the images were modestly-sized. None were larger than 150 Mbytes. So I did the dumb-luck thing and re-opened the HTML using Word, and saved the whole mess as a Word file. The new file is 2.6 Mbytes!

When a Word (or other Office) file is saved as HTML, all embedded objects are saved as separate files in a subdirectory with a name derived from the document's name. That is where the images were put. Some were GIF, most were PNG (similar to GIF but some files compress better that way), and a few were JPG. The HTML conversion does optimization of its own. In this case, the final compression factor is about 50. I don't know why. I don't plan to go to the work to figure it out, either. That'd be looking a gift horse in the mouth.

I have since used the Compress Pictures to save space for several files, and I'll keep the to-and-from-HTML method in reserve in case I get another pathological file.

Thursday, September 11, 2008

Medicine, shmedicine

kw: book reviews, nonfiction, alternative medicine, medical studies

I visited a chiropractor a few times, when several sessions of physical therapy did nothing to alleviate neck pains. I know what the problem is: all day looking at a computer screen and lots of evening hours reading. I do various stretching and loosening exercises, but little relief results. Nothing has really worked except copious intake of ibuprofen. So I asked my family doc if he thought chiropractic would help, and he said it was worth a try.

I'd heard a talk by a chiropractor who claimed to distinguish between "manipulation" (forcible) and "adjustment" (gentler) of the spinal joints. I went to see him, and he started by using some electrical device connected to his computer to map my spine. The device seems to measure nerve impulses and muscular twitches or heat. It showed where I supposedly had nerves being pinched. I'll come back to this.

I'd heard about the risks of manipulating the neck joints, so I asked him to refrain from any but the most minor "neck work". As it turned out, part of each therapy session was five minutes of massage, and this did me more good than anything else. However, the chiropractor gradually ramped up his procedures as he thought I was tolerating them. At some sessions he did some milder "neck crack" moves that I judged within the safe zone, but I could tell he was gradually increasing them.

At my last session, he used more force than I wished, and ended with one of those wrap-arms-and-crunch-in-mid-spine moves that really hurt. It also made a loud pop. He looked so proud of himself that I was speechless. I picked up my coat and left, then phoned back that I would not be returning. The spot he crunched hurt for three days. Again, none of this alleviated my neck pains, except the massage. But my insurance program will not pay for massage-only treatments, even "therapeutic massage".

Like nearly everyone, I've had various other encounters and experiences with alternative medicine. The most bizarre was the tendency of my mother to follow the advice of Adelle Davis (main book, Let's Eat Right to Keep Fit, with almost religious intensity. Fortunately I'd moved out by the time she began to concoct a protein-vegetable juice mix my younger brothers called Lion Milk, and which they loathed. Proper nutrition is good, but I've determined that much of Ms Davis's advice is scorned by real nutritionists, such as taking lots and lots of extra calcium if you have arthritis—you need instead to do something about how your body uses the calcium it has already (maybe she mistook arthritis for osteoporosis...?). I do take some nutritional supplements, and that is fodder for later on also.

Chiropractic is one of four major alternative medical methods discussed by Simon Singh and Edzard Ernst in Trick or Treatment: The Undeniable Facts About Alternative Medicine. The other three are acupuncture, homeopathy, and herbal medicine. They also have an appendix with one-page surveys of thirty-six less prominent techniques and methods.

Their first chapter is a very good discussion and explanation of evidence-based medicine and the scientific method, introduced by a cogent quote from Hippocrates:
"There are, in fact, two things, science and opinion; the former begets knowledge, the latter ignorance."
So what is evidence-based medicine? It is the application of genuinely scientific methods to the study of medical therapies. The biggest hindrances to such work are
  • The placebo effect, which expresses the tendency of a treatment to cause improvement solely due to the expectation of the patient that "something is being done."
  • The Hawthorne effect, which is the tendency for a person to respond positively to any attention at all, as compared to being ignored or getting little attention.
Thus, human effects can totally swamp the effect we are trying to evaluate. For this reason, a proper scientific study, called a clinical trial when it is medical, must have these elements:
  • A sufficiently large group of patients that good statistics can be produced. For example, the expected scatter in numbers "helped" is about ten if 100 patients are tested, and about 30 if 1,000 are tested. Thus if you give treatment A to 100 people and treatment B to another 100 people, and the difference between those who improve is less than ten, you can't say there is a useful difference. However, had you used two groups of a thousand, and the difference is something like 100, this is much larger than the expected "error" or scatter of 30, so you can say you have a useful result.
  • Proper control: One treatment is either a known treatment with known efficacy, or is a non-treatment (a sugar pill or water injection for example), while the other is the treatment being evaluated.
  • None of the patients knows which treatment he or she is receiving. This means the placebo effect will be the same for both sets of patients.
  • None of the doctors performing the treatment knows which is which either. This means the treatments must be prepared by a third party and given to the doctors in a way that doesn't clue them in. This means a treating doctor won't behave differently with one or another patient, so this negates the Hawthorne effect. These last two points are the "double blind" you might have heard of: both doctors and patients are blind to what is being done to whom.
There are many clinical studies of all kinds of alternative therapies. However, there are very few that fit the criteria above, and in particular, even well-controlled and blinded studies often had too few patients to produce good statistics. But a method called meta-analysis can combine the results of several studies to produce better statistics. One study with two sets of 100 patients may not yield a definitive result, but if there are ten well-done studies that total two sets of about 500 or more, the statistical power is multiplied.

So what is the result? Of the four major areas of alternative medicine, only herbal medicine has any effective treatments, and only a very few of the many herbal medicines being sold can be said to help by any measurable amount. Secondly, chiropractic treatments can help some cases of back pain, but only a little more than just resting the back for a few weeks.

The authors have bent over backward to avoid their own biases, and give credit where it is due. The one area in which no credit due can be found is homeopathy. This is the practice of taking a substance that, in some quantity, will cause the problem being observed, and using a very small amount for "like treats like" therapy. For example, ipecac causes vomiting, so the idea is that a tiny dose of ipecac might alleviate a vomiting spell. However, homeopaths take that word "tiny" to an extreme. They use successive dilutions to produce "medicines" that probably don't contain even a single molecule of the substance.

For example, to make a homeopathic ipecac tincture, put 1g of the syrup in a liter of distilled water. This is a 1/1000 dilution. Put one gram of this stuff in a liter of distilled water. The new liter's dilution is 1/1,000,000. Repeat ten times. The number below the slash now has thirty zeroes. The trouble is, the number of molecules in the original gram of ipecac is a number with 22 zeroes. That means, if you were to prepare 100,000,000 liters of the final dilution, there would only be one of them, or perhaps two, that contained a single molecule of ipecac. The rest would be pure, distilled water.

This "medicine" might be sold for $50 per liter, making that single molecule of ipecac worth billions of dollars! The primary disease that homeopathy treats is an excess of riches. This may seem to be no more than a harmless placebo, but if a person trusts only homeopathy when there is a real, but treatable, condition, an unneeded tragedy is likely.

There is a ray of hope for alternative medicine: every genuine remedy began as an "alternative", and most of our effective medicines are either plant extracts or are derived from them with a little chemistry. For example, aspirin is a chemically-modified version of salicylic acid, which has much more severe side effects. Yeah, aspirin might cause a bit of stomach bleeding in some folks, but the raw acid causes lots of stomach problems in almost everyone. So there is always a chance than a treatment now considered "alternative" will someday become "normal medicine".

However, even though some herbal medicines are effective, most have troubling side effects. Let us remember, plants have no incentive to produce chemicals which are good for humans. All the chemicals they produce are good for themselves. A few are incidentally helpful for our uses. I don't like to hear, "But this stuff is Natural!" So is nightshade, which will stop your heart; so is strychnine which will either kill you, very painfully, or just ruin your brain so your loved ones have to take care of a near-vegetable for a few decades.

The appendix summarizes 36 treatments, of which these few are at least a little effective, and their side-effects are at least not deadly:
  • Aromatherapy can help you relax, but has no other benefits.
  • A few techniques of Ayurvedic medicine are a little effective, but most are without value. Lotsa studies are needed to figure it all out; it is even more complex than Chinese medicine. Chinese medicine is treated in passing in the Herbal Medicine chapter, and is a similar situation; too complex to deal with as a whole.
  • Some Food Supplements are helpful, but very few of those that are not known to be vitamins are any good at all. Be careful not to overdose, particularly on the B vitamins.
  • Hypnotherapy and Autogenic Training (self-hypnosis) can help you relax, and that's the limit of their effectiveness.
  • Massage Therapy, ditto, also as attested by my experience.
  • Meditation, double ditto.
  • Osteopathy, because it is not just skeletal but also takes account of the muscles, can be more effective than chiropractic for spine and joint pain. I used to see an osteopath as my primary physician, and he showed me an exercise for sciatica that is very helpful.
  • Relaxation therapies...did you note that five of these items are for relaxation. Many of our aches and pains can be helped by a little relaxation and rest. To those who like Biblical examples, Jesus frequently took his disciples out to the desert to get away from the stress of dealing with crowds. It didn't always work, but he practically invented the Retreat.
Now, if you've read this far, and want to know more about my experience, I find the spine-measuring device rather fascinating, but I don't for a minute believe it does what its proponents say it does.

The chiropractor pressed a probe with two low metal buttons against each joint between vertebrae, and held down a foot pedal while watching a wavy line on the computer screen. When he let go, a number got recorded. It didn't take long for me to figure out that he was letting the waviness settle down, but usually not for long enough to get a really stable number. I have pretty good short-term memory, so I could see that his early stoppage of the reading had more to do with the final number than if he'd let the waviness really settle down, which he occasionally did. Had he done so throughout, my spine's report would have been pretty bland. A repetition of this test after several sessions seemed to show I was improving. You couldn't prove it by how I felt. The only time I felt better was the ten minutes after a bit of massage, and before any "adjustments".

I think that, at best, the device used is more like a Ouija board, producing results that arise in the doctor's imagination rather than the patient. At worst, it would be easy to produce any result you like. Just a little difference in pressure changes the range of the wavy readings quite a lot, and the timing of "release" can produce almost any result also. So I still have my neck pain, and probably will until I retire. The only thing that alleviates it is to rest with my head propped up just so. I can read in such a position, so I do more of my reading while reclining these days.

Now as to supplements.
  • In addition to a multivitamin I take "just in case", I use a Glucosamine/Chondroitin pill for my joints. I had a bad shoulder for ten years until I began using these, then in a few weeks I got better. Too bad they don't do anything for my neck (or maybe it would be lots worse?!?).
  • I also use extra calcium, at my doctor's recommendation.
  • Finally, I use a large amount of an Omega-3 fish oil extract, also my doctor's idea. This last plus exercise seems to be making by blood chemistry better than a cholesterol medicine I took for a few years, and I weigh less now because the cholesterol medicine boosted my appetite, a lot.
Finally, a specific warning: There is a popular Chinese herb called Aristolochia or birthwort or pipevine. Don't use it. It has killed numerous folks by destroying their kidneys, over a few months' time.

Wednesday, September 10, 2008


kw: neat things to know

My brother sent me a remarkable 60-page special edition of Wired that contains the contents of Geekipedia as it was originally released. It is growing.

Link in and look around. One of the newest articles is titled PICNIC, an acronym for Problem In Chair Not In Computer. While it can be used as an insult similar to "The problem with your car is the nut that holds the steering wheel," it is used in the tech support community to refer to an apparent problem that is most simply resolved by educating the caller a little bit. The article on Quantum Computing explains why it is still worth following.

Each article includes a button: "Suggest an entry", but be prepared to have a really good idea. The editors of Wired want Geekipedia to be really useful, not just a geeky clone of Wikipedia, which they see as bloated, having a few pithy nuggets awash in mediocre or uninteresting articles. Personally, I don't browse Wikipedia, I search it, so what I find is typically of great interest and use, at least to me. Having the 2007 version of Geekipedia in print, I'll read it all.

Monday, September 08, 2008

To accompany the BIG guys

kw: book reviews, nonfiction, whales, music

Thousand Mile Song: Whale Music in a Sea of Sound by David Rothenberg is not about whale sounds per se, but about whale-human musical collaborations. Or, at least, attempted collaborations. The book includes twelve tracks on a CD. Two of the tracks include no whale (or other nonhuman-animal) sounds at all; one is a riff by two musicians on the feelings inspired by a few months of listening to whales, and the other is a whalesque accompaniment to a song Pete Seeger wrote but never recorded, "The World's Last Whale." Seeger, being 87 at the time, declined to record it this time also, so Rothenberg's voice is heard instead.

As well as I can infer, the author was occupied for two or three years with planning and carrying out three major field expeditions. Recordings from these and from material placed at his disposal by others was used to produce the CD.

Throughout the book, Rotherberg recounts the stories of whale sounds and the surprisingly short time that they have been acknowledged by Westerners, though other peoples have records and legends of whales singing that go back centuries, at least. Whale song mby be behind the legends of Sirens. Considering that a singing humpback whale can literally shake a dory with its song, it is amazing that nearly no Europeans listened or even seemed to notice until the 1940s.

A characteristic attitude is displayed by many who now study Sperm Whale sounds, which are strings of clicks, both steady and syncopated. They consider that louder, steadier clicks are for echolocation ('sonar'), and quieter, more amorphous click strings are social in intent. However, the former are heard most often in social settings! Scientific training seems to predispose the mind to "either-or" thinking, but more inclusive thinking is called for here.

Humans use sight much more than sound for gathering information. Imagine someone saying that the glances we take in social settings are mostly for keeping our physical balance and finding our way around. True, some are, but most are socially motivated: checking out another's feelings towards us, leering or ogling, flirting or connecting, or looking for agreement. I have read that a whale or dolphin can see the insides of another; it is hard to keep secrets when your heart rate can be counted! If you hop into the water in an angry frame of mind, a dolphin will know it by the shape of your viscera.

Anyway, the author's interest is primarily to play ensemble music with whales. Listening to the CD, I can't be sure if he succeeded, and while he feels he did, just a little, he is not totally certain. A whale's emotions seem to be as unfathomable as its thinking. That hasn't changed, but the music is pleasant, and it is probably a bit more collaborative than playing a clarinet along with the moaning of the wind in the trees.

Friday, September 05, 2008

One person's fat-to-fit journey

kw: book reviews, nonfiction, obesity, self help

I've worked with a man who usually weighed 400 pounds or more. It was compounded by his short statute, no more than five feet eight. Convert to metric and figure BMI: 181kg / (1.73m)² = 61. Considering that the "standard" defines BMI>40 as "morbidly obese", I was amazed that he'd lived nearly sixty years. I remember that he ate almost constantly. I suspect he didn't pay much attention. Yet he knew he was "really, really fat". It seems he'd long since given up "reducing", and did a lot of walking to keep in some kind of shape. Thus he was in better condition to be out in the world than was Susan Blech in her mid-thirties.

As she reports in Confessions of a Carb Queen: the lies you tell others & the lies you tell yourself, Sue Blech passed 400 pounds about the age of 35, and weighed just over 468 pounds (212kg) by age 38, when she entered a "fat farm" clinic in North Carolina. She never mentions her height, but if it is near the average for a Caucasian woman (65 inches or 1.65m), her BMI was about 80! She also reports that it was very hard to walk, and she seldom left her apartment. She was well on her way to becoming first a quarter-ton, then a half-ton homebody. The heaviest verified weights are 1200lbs (544kg) for a man and 1190 lbs (540kg) for a woman: both well over a metric half-ton and both bed-bound.

As the author, with her sister Caroline Bock's help, reports in her first eight chapters, she spent up to four hours daily going from BK to Wendy's to McD to various pizza places, eating meal after meal, and "grazing" almost constantly betweentimes. All the while, she would say she was "a little chubby", always "on a diet", forever promising herself to "do better" at some later date, usually the upcoming Monday. Finally, at age 38, she realized, "As I get bigger, my life gets smaller." Spurred by the fear that she will have a stroke and end up like her mother, incarcerated in a mental hospital after a stroke in her 40s, she went for help.

She entered a weight-loss clinic in Durham, North Carolina where, over two-and-a-half years she lost 250 pounds. It wasn't steady going, and she had binges once or twice. With the help of friends she continued to battle. She had those she could call when she got home to report that she was safe: "'Safe' doesn't mean that I wasn't in a car accident; 'safe' means that I didn't stop at Wendy's".

Some have written that lying is one thing, but when we believe our own lies, that's obsession. She had been obsessed. She is frank that she was very seldom hungry. She didn't eat from hunger. She ate for comfort, the comfort of a motherless child whose father comforted his children with food. Yet her three siblings didn't become obese. As the youngest, perhaps she felt most keenly the loss of her missing mother, still alive but still rarely aware as the book was published. She reports that the only way she could sleep was in a calorie-induced coma.

She herself doesn't know how she was able to sleep under the clinic's regimen of little more than rice, grits, and water. Initially, while getting used to it, it was probably only total exhaustion. But she also got a personal trainer, who patiently urged her to greater and greater efforts until she could sleep from genuine fatigue. She'd been an athlete and bodybuilder in her 20s, so whe knew how to exercise. As she reports, she found she needed a "boss", just like at any job.

The book opens with a small picture of her, an anxious-looking figure in front of a door. She is exactly as wide as the door. It closes with a larger picture of a much more slender woman, one who looks really good at 210lbs (95kg). She is a pretty woman at either weight, but is much more appealing as a "merely large" forty-year-old.

She makes it clear that she is no expert on weight loss, but only an expert on how she lost weight. Bread triggers her obsession. Total expulsion of bread from her menu is a major key to her success in losing weight. Each of us must clear-headedly figure out what our own obsession is, or we'll go through life never knowing how much we are deceiving ourselves. Sue Blech's inspiration is rooted in knowing that it is possible to recover from obsession, and thus recover from the symptoms that follow.

Wednesday, September 03, 2008

The second most studied creature

kw: book reviews, nonfiction, microbiology

The most studied creature is, of course, the human animal, ourselves. The second most is a much smaller item indeed: Escherichia coli. Adult humans mass sixty to a hundred kilos; an individual E. coli bacillus masses one or two trillionths of a gram (1-2 pg, pg=picogram).

These E. coli colonies in a petri dish were sent by NASA aboard the Genesat satellite experiment in December, 2006. In his new book Microcosm: E. coli and the New Science of Life Carl Zimmer doesn't mention Genesat, but he discusses just about everything else regarding this little bug. A few highlights:
  • Every human carries from a few grams to a kilo or so of them in our colons. At a trillion cells to the gram, they number a hundred to a thousand times the number of humans on the planet—in each of us.
  • The number of human cells in a typical human is less than ten trillion.
  • The prevalence of E. coli in experimentation is mostly because they are one of the easiest organisms to grow in large quantities.
  • A well-fed colony of E. coli can double in mass every thirty minutes. Given food enough and a sufficiently "swirly" mixing environment, a single cell could thus grow to equal the mass of the earth in just 66 hours, or less than three days.
  • A number of terrible disease-causing bacteria that were once given names such as Shigella, have now been found to be strains of E. coli. The O157:H7 strain is a fearsome beast, one of the "flesh-eating" bacteria. You can't use antibiotics against it, because the toxins released during its death throes kill the host (you, if you're infected!).
  • Relatively cheap insulin is just one product used by millions, that is now produced almost exclusively by genetically engineered E. coli, grown in huge vats.

This bit of time-lapse imagery shows initially three cells on the verge of dividing. Decoding the times, successive images were taken after 12, 17, 33, 80, 97, 109, 115, and 179 minutes. By 97 minutes each original cell has become four, and several of them are about ready to divide again. By the end of the series (179m = 3h), they are getting hard to count; I make out 54.

The images are phase-contrast micrographs and if your monitor's resolution is 100dpi (4 lpmm), the magnification is nearly 1000x. These are pretty good images for a light microscope. Without phase contrast, the cells are nearly transparent, though with dark-field illumination they aren't hard to see. I don't have a phase-contrast setup, but I do have dark-field capability.

This 2000x image (somewhat greater than 3000x in the larger image you get by clicking) is about the best you can see E. coli using light. Better resolution requires an electron microscope...not to be found in any homes I know of!

Carl Zimmer's emphasis is on the history and sociology of this bug, so he doesn't have the gallery of photos one might imagine. He does have a compelling series of chapters that outline the way this amazingly versatile critter works...to the extent that it is known to date. He clearly makes the point that E. coli is far from a "primitive germ": it is the product of four billion years of evolution, just as we are, a very sophisticated generalist of a germ. It lives not only in the human gut, but in the gut of every warm-blooded animal on Earth. And that is just the "mostly harmless" strains (though fearsome O157:H7 lives in farm animals, it doesn't harm them...not them). Other strains are found in "external" environments worldwide. It can live with our without oxygen, at a wide range of temperatures, and it can feed on quite a variety of organic chemicals in addition to its favorite sugars.

It is the first prokaryote ("pre-nucleus") to be shown to engage in a single-celled version of sex. So promiscuous is it on that it exchanges DNA with quite a variety of bacterial species, to the point that there is a serious effort to redefine "species" for prokaryotes. DNA-trading, both voluntary through "conjugation" and involuntary due to viral activity, causes a huge amount of "horizontal" gene flow throughout the whole microscopic domain.

Perhaps this very promiscuity is the safeguard that keeps our engineered strains of E. coli from going wrong and screwing up our world. They've already figured out, billions of years ago, how to share genes in every direction without screwing up their world. We get a free ride. And this same promiscuity has made them the ideal Frankenbugs: it has become almost easy and quite cheap to coerce them into bearing and expressing almost any gene we like...with a big proviso.

Sugar. Eukaryotes ("good nucleus" – all life bigger than bacteria) have developed ways of decorating proteins with sugar groups, which changes how they fold up. This is essential for making many proteins work right. Prokaryotes (so far as is known) don't add sugars, so much work is being done to either teach them the trick or to modify them to use extra amino acids with sugars pre-attached. We were lucky that insulin doesn't need to be glycosylated (sugar decorated) to work.

There is no single photo that shows everything about the bacterial cell. For one thing, E. coli looks different depending on its environment. This cell (magnified ~10,000x) is in a social mood, ready to bind to others to form a biofilm. Isolated cells going about their own business don't have these pili (hairs).

Do you know what a biofilm is? The next time you floss your teeth (you do floss, don't you?), take a second to look at the whitish goo that was between your teeth. Dentists call it "tartar". It hardens into "plaque", which has to be removed with a dental pick. Both tartar and plaque are biofilms, and there is no safe, chemical way to remove them. Floss and dental-picking are the only known methods.

Perhaps you have a plastic shower curtain that never quite dries out at the bottom, and it's getting slippery. I do. That slippery film is a biofilm. The buildup of "stuff" on the surface of a porcelain sink, that you need to use cleanser and a sponge to remove, is a biofilm. Bacterial cells have settled down, linked together a lot like locking arms, and excreted starches and sugars to hold them to the surface and shield them from enemies and chemicals. Biofilms are probably the normal mode of life for most bacteria; the single ones we see illustrated in textbooks and encyclopedias were on the move, getting ready to settle down.

But illustrations such as this painting, composed of information gleaned from numerous images, help us see what the cells look like. The trailing strands are flagella, which the cell forms as needed when it must travel. When the critter settles down, it sheds its flagella

The colors in this image are fanciful, shown only to enable easier grasp of details. The only colors present in real E. coli cells are the creamy or golden yellow seen in colonies like those shown in the first image above. There is so little color in a single cell that under the microscope they look clear or slightly grayish, like elongated drops of water...very small drops.

One final thought I find fascinating. A single strain of E. coli has a genome consisting of between 4,000 and 6,000 genes (maybe a wider range than this). Some strains have as many as 1,000 genes not found in any other strain, and some share fewer than 2,000 genes with the "pangenome" of E. coli, the total collection of all known E. coli genes, which numbers nearly 20,000 to date. As it happens, there is every likelihood that the E. coli pangenome is greater than the human genome. Now that is both exciting and scary. But I also wonder, are there genes that some people have and not others...and how extensive is the human pangenome?

A more likely response

kw: opinion, politics

In my previous post, I outlines two scenarios that might follow the pregnancy of a candidate's child, if it occurred on the Democratic side. As I wrote, these scenarios were based on the public social positions of the present and former candidates. However, I don't really think the Biden or Obama family would actually behave that way (the Clintons just might). In my experience, when it is their own family on the line, folks are quite a bit more conservative than they are when giving speeches or formulating policy.

Thus I would not expect much difference between the possible actions of the Obamas or Bidens as compared to the Palins, and Senator Obama's statement regarding the situation supports my expectation.

Tuesday, September 02, 2008

Doing the right thing anyway

kw: opinion, politics

I seldom comment on the political scene, but this time it is personal. I know from the inside the family dynamics that occur when a member has strayed and will have to live with the consequences. This is the case with the new Republican Vice-Presidential nominee, Sarah Palin and her pregnant daughter. It has been announced that the daughter will keep the baby and marry the baby's father, and that Senator McCain knew about the situation beforehand. I see this as a remarkably responsible response by Governor Palin and her family.

It is no surprise to me that the Democratic Party leadership is forging a scandal about this. Of course, it actually is a bit of a scandal, but a family one, not a political one. The real scoundrels here are those making hay out of this.

Let's just consider if a young pregnant woman whose surname happened to be Biden, Obama, or even Clinton, were "exposed" at this juncture. What would be the result? Based on the public pronouncements by the Democratic candidates and former candidates (and a former President), one of two possible scenarios would ensue:
  1. A behind-the-scenes "How dare you endanger this campaign" conversation, followed by a hushed-up abortion.
  2. Perhaps the same conversation, perhaps not, but then a very public "Our daughter will raise this baby herself," with the implied, self-congratulatory attitude that no man need be involved.
Both scenarios are fully in keeping with the social policies of the far Left, and both are deeply irresponsible. Say what you like about Conservative politics and social policies, Conservatives are strongly for taking responsibility for your own actions, including doing what you can to correct of ameliorate your mistakes.
  • Admitting the facts is responsible.
  • Declining to "correct the problem" via abortion is responsible.
  • Advising a young couple to enter into a very young and risky marriage is more responsible, compared to the tendency to forbid the young people to see one another. The baby is likely to do better with two natural parents than in most adoptive scenarios.
  • Pledging familial support and encouragement to the young couple is responsible.
However painful this may be for the two sets of parents involved, they are taking the right course. If anything, this incident strengthens my confidence that Gov. Palin is a very good choice for the "heartbeat away from the Presidency."

Monday, September 01, 2008

Another College year under weigh

kw: musings

Yesterday afternoon, we piled two cars with our son's stuff and drove up to move him in for his Sophomore year. His campus is less than two hours away, so visits, either direction, are easy. But he has a life to learn to live, so we don't go up more than once or twice per semester.

Last year we were surprised how quickly we adjusted to seeing him so seldom, and having an effectively empty nest for nine months...and how hard it was to re-adjust to his presence for the summer! I guess, because we were married more than twelve years before he was born, that we already knew how to operate as a 'single couple'. We just celebrated our 33d anniversary, and our son is just a month shy of 20. Old habits came right back.

He has two of the same housemates this semester, and will be getting a new one, maybe two, but they are all guys he knows. He's been going up to the area at least a couple times a year with church groups since he was eleven. So he also adjusts quickly.

After getting him moved in and rousing his household to do some cleaning, we all went to a home nearby that was having "Frosh Welcome Nite" with a Mongolian hot pot feast. It is a favorite with the students...and we enjoyed crashing that party very thoroughly. It turns out my wife and the woman of the house had met each other more than twenty years ago, so they had a great time re-connecting.

Hot pot dinners are fun. Several boiling, soup-filled woks are laden with fish balls and a few other favorites to get things started, and the tables are full of little packages of raw seafoods, meats (thinly cut), vegetables and tofu. The main rule is, put as much into the pot as you take out. So people alternately stand to grab food and dump stuff in, and sit to scarf it down. Lots of talk, arguing over what to put in next, calls of "who wants some of the shrimp; they're ready", and horse trading of favorite foods. Everyone has a little bowl of a special spicy sauce to dip everything in. There were about 30 people there, so it was quite a hullabaloo.

We left just after 8 pm so we'd get home by 10. Today I need to dump some shekels into his account for books, and by Wednesday he'll be deep in studies again. I hope this year goes as well as last year.