Science, sometimes.

Other bloggery, and stuff

2011-02-19T14:02:00.004-05:00

I have another blog that details some of my machining and electronics projects. I plan to keep this one as a kind of place to philosophize and pontificate, but I hope people find the other interesting as well.

Writing, Here and There

2010-12-01T23:55:00.003-05:00

Clearly, I have been less than serious about this blog for quite a while. It is not that I have ceased writing, but rather, I have been writing different things, different places.

For example, I have a series about energy usage at the world.edu website. I'm trying to help people make sense of the details of alternative energy proposals. One in the series can be found here.

At the same time, I am going to pick up where I left off here, and I'll link to some writing I am doing about my adventures in my garage machine shop.

Happy Blogiversary

2010-02-24T02:00:00.002-05:00

I've been doing a half-assed blog for five years now. You can see the initial post here. I haven't kept up because other things, like Facebook, occupy most of my non-technical computer time.

CyberPolitics

2009-06-20T23:55:00.003-04:00

I have been fiddling with Twitter for months now, and frankly just could not find anything engaging about it at all. I kind of liked the simple API that it has, but at the same time, the idea that Twitter is just, well, dumb, was reinforced by techies doing things like setting up their toilet to tweet when it was flushed. There is a portion of this that I admire; I think that more and more of the things in our environment could be set up to communicate to make life easier and better. Doing an 'art project' of this sort helps expose the problems and possibilities of existing communication standards. But this is sufficiently tasteless that it decreased my interest in the technology for a while. I didn't care to tell anyone when I was going somewhere, and couldn't imagine caring what anyone else was doing trivial enough to be encoded in just 140 characters, and I sure as hell don't need to know when someone is on the crapper unless we have to share one.

Facebook has been a lot of fun, so it isn't that I am a social networking curmudgeon ("Hey you damned kids, get your Web 2.0 off my lawn!") and although the status line is roughly analogous to tweets, Facebook has a lot of other things going for it. I'll leave my musings on FB for another post, because it has something interesting going on too that I want to think aloud about.

Anyway, with the recent unrest in Iran following the apparent re-election of Mahmoud Ahmadinejad, I kept hearing that the Iranian people protesting the election, which they said was fixed, were communicating via Twitter. I was not sure what to make of this, so I looked in, and it dawned on me over the course of a few hours (of following with rapt attention, tweets that contained links to cellphone video and news stories) that this was something of great importance. Twitter may not have been intended to be this kind of tool, but many things find their best use only after having been around a while.

What emerged was that this technology provides a quick and easy way for people to let the world know what is going on. One might expect that the mullahs would just pull the plug on all of the communication and internet resources that allowed this. But this is where the politics gets interesting.

To some extent, all of the things that Ahmadinejad and the mullahs have been doing with respect to nuclear enrichment have relied on having a digital infrastructure in place. They cannot just shut it off without screwing themselves. So they shutdown or block servers that carry digital traffic outside the country.

Twitter matters because people on the outside can help, by setting up software to provide misdirection, anonymity, and proxies so that bloggers and tweeters in Iran can bypass the routes that have been restricted by the mullahs.

Twitter matters because 24 hours ago, I had never heard of Tor, and had only the vaguest idea of how to set up proxies (my 12 year old already knew, but that is another story). Now I have several things set up to try and help.

A friend of mine and I had a spirited debate over whether Twitter was helping. He seemed to think, from what I can tell, that the fact that 90% of those tweeting support couldn't find Iran on a map, and didn't know anything about Iranian politics, meant that they should just shut up and get out of the way. But the point is that people are watching, even if they do not know what they are seeing. They can certainly understand a bystanding young woman being shot on the street by the government.

I don't have a dog in the Iranian election fight, and it might well be six of one, half dozen of the other when it comes to who won. I don't know enough to speak about what is going on.

But I do support peaceful assembly, and free speech, and I don't think these sentiments are just products of American cultural imperialism. There is a Universal Declaration of Human Rights, and peaceful assembly and free speech are in it. So I want to help, and will, in a tiny way, knowing that my servers are not going to change the world. But enough drops fill buckets.

Religious Wars

2009-05-25T11:51:00.003-04:00

I work at a place that is 100% Windows OS driven. Despite Microsoft's release of Vista, we are solidly XP Professional.

When I chose a computer for home, I picked an iMac. With the advent of Apple's OS X, with its core based on the unix-like Darwin (nee' Mach) operating system, I was attracted to the chance to use a *NIX box and take advantage of the multitude of software available. It is a bit harder slog, if one opts to download and compile source code for thing, but it is a very good, and very educational, way to work. And the native OS X look and feel is very good. I won't say better than XP, although I prefer it. I will remain unchurched in the OS religious wars.

Still, there are things available on XP that I like. I have had a lot of fun, and learned a great deal, using Microsoft's Express Editions of their compilers for C++ and C#. It is not impossible to do the same sort of programming on the Mac, and I am learning some of this, too. But MS has a pretty extensive evangelization effort for their compilers, and there is a large body of work that I wanted to take advantage of, so I had been doing some development on my XP laptop.

However, I recently discovered something called VirtualBox, a Sun Microsystems product that allows one to run other operating systems (called 'guests') under an existing operating system (called the 'host'), like *nix or OS X. I got a copy of Ubuntu linux and began running it, and was impressed by the performance, so I decided to get a copy of XP and load it as well. Having seen it work with Linux, I was not too surprised to see XP boot without a hitch.

VirtualBox comes with software called "guest additions", which allow certain guest operating systems tighter integration with the host, and with the underlying hardware. In the case of XP, this allows some access to serial and USB ports, and allows more screen resolution. Apparently it makes things faster, but I installed them immediately, so I didn't see.

Despite running beautifully on my Mac, all the pointedly irritating things about XP persist. Connecting to a network printer was far harder than it should have been. I set up the damned network here, and my Mac and my wife's PC (where the printer is located) are not 6 feet from one another. I fiddled with it for half an hour, but it did eventually work.

From a philosophical point of view, there is something awesome about virtualization, running an OS on another OS. As hardware become ever more powerful, we can make any hardware look like any other hardware to software. I am not doing this idea justice by sitting here, slack-jawed, but at the moment, that is all I can do.

Computing

2009-05-25T01:32:00.003-04:00

About 60% of what I do every day at work now involves me writing software. Of that, the largest part is LabVIEW, but this has begun to expand into C++ and C# as well. There is a tremendous amount of overhead involved in writing software, but the payoff is that once the programming is finished, if it is well-written, it is possible to get data at a rate unimaginable in the absence of the automation the software provides.

That describes pretty well why I put up with writing software- automation of data collection makes it worth the headache. Only, as I do it more and more, it becomes much less of a headache, and something altogether different. It has become a means of thinking about the world. The algorithmic mindset, I find, complements the scientific. I have heard it said that programming should not be an experimental science. Well, in the hands of an experimental scientist (at least this one), it most certainly is.

I cannot imagine programming to do something like accounting or database management or business systems, though I am quite happy to use the fruit of such labor. It would not be something I could stomach, I suspect.

But getting things to do stuff...this is intoxicating, and I like it a lot.

In the process of doing experiments, I have learned a little about programming microcontrollers. I can't pretend that programming a microcontroller to run a dishwasher sounds like crazy fun, but it doesn't sound bad, either.

The key is that the combination of software that allows one to control things, coupled with chemical and other scientific knowledge, allows the creation of systems of fairly awesome power. I am keen to try to learn more, and hopefully post some of my non-professional experiences here. "The man" owns my professional experiences. Not that I am complaining. I'm pretty happy to be in the employ of "the man" in times as tough as these.

Once again, into the breech...

2009-03-09T20:30:00.002-04:00

I think I've neglected my blog long enough. I have had so few readers that I had no real issue with setting it aside a while, but now I am thinking of how best to use it. I am not fully decided, but I want to focus on chemistry and science in general.

For now, I'll just post my intentions. I can't quite break away from other commitments just yet. But I'll be back.

JavaScript

2008-11-25T10:18:00.004-05:00

__________________________________________________

This is my first foray into public javascript programming. Now, the above example is pretty silly. But until recently, I had not been able to use javascript in Blogger pages. Stay tuned, things will become more interesting.

Empowerment

2008-11-15T18:33:00.002-05:00

I use computers all the time. I often find myself struggling to learn the fundamentals of a new programming language (last year I picked up a working knowledge of Java, and at the moment, I am beginning the same process with Python). The internet has made this progressively easier, because there is a dizzying array of information and tutorial material available, much of it free, or nearly so.

Both Java and Python are free. I can get anything I need to write programs in these languages for free. This alone is remarkable, but the power that these languages have, especially their friendliness and built in support for web programming, makes the head smacking that goes along with learning anything complicated well worth the dents in my forehead.

I am not a professional programmer by any means- I am a chemist (and fiercely proud of it!) If I want to learn something new in chemistry, I have the background and experience to pick up the greater fraction of what I need to know from reading. The last 15 to 20 percent, however, is best learned by talking to another chemist skilled in the technique or area, and even better, watching them set up a reaction or do a measurement. If you have a huge Karmic bank account, and they will watch you do it, and offer critique, then you are as close to heaven as you can get and not have wings.

I don't have easy access to professional programmers, even though I work in the same building with a bunch. They are busy, and we do not necessarily cross paths. I can't readily ask them things without disturbing their work, and watching someone program is boring and largely unhelpful. And probably pretty creepy for the person being watched.

I discovered a very cool website called ShowMeDo that contains all sorts of tutorial screencasts about various programming topics. They are done very well, as far as I have seen. Much of the material can be accessed free of charge, but for a modest subscription ($60/yr) you can get access to much more, as well as having your feedback considered in new rounds of content creation.

A tool like this is invaluable- $60 is very reasonable, less than the average I would pay for a programming book at the local bookseller or on Amazon. Certainly, the books are more comprehensive, and as I learn what I am doing, just like with Chemistry, I can look up most of what I need to know. But "Monkey See, Monkey Do" is still the most powerful way I know to learn things in a hurry.

Googling

2008-11-12T23:14:00.002-05:00

One of the things that strikes me is how much more computers have become than I ever imagined. I had no doubt that they would be powerful and useful and interconnected. What I did not anticipate, at all, was how much would be possible effectively free of charge.

My son and I use Google Calendar to keep track of his homework assignments. I use it to keep a calendar of my own, one that will email and text me if I set a reminder. I can text items to my calendar, and within reason, the calendar application will parse what I send it and insert the new item into my schedule.

I have a blog now that I am working on as a message passing system. I email or text messages to SMS Data Collection. I have some Google spread sheets set up to retrieve and parse this data. So far, if you bother to go to the SMS Data blog, you will see nothing of interest. I am doing all of the data sending by hand, largely just to work out the details of how to retrieve and chop up the data. Even after I get things going, there won't be much to see, and a lot of it may be quite cryptic. I am just using it as an intermediary.

There are a couple of things I plan to do. First, I have an idea for keeping track of a vehicle on a road trip. This device here will get GPS data and text it to the blog. A Google Documents spreadsheet will periodically go and get the data and parse it into pieces that will tell location, speed, and so on. This will feed a map that people that are invited will be able to look at, showing our location and anything else I decide to . I imagine using it as a way to keep my Dad updated on progress when we drive home, and as a way to post pictures and routes when we go to Canada or out West.

Various programs that take data for me, using LabVIEW or other software, can also email stuff. All of this can be processed using free, readily available web software and turned into something anyone with access to the Web could potentially use.

The fact that so much of what is available is opening up to being programmed by people who are not necessarily professional programmers is particularly exciting. The ability to use the power that exists in technology has resided in a subset of people that doesn't necessarily overlap with the subset of people who might do really interesting and creative things with the technology and data. The leveling of this, so that one need not be an acolyte of the computing profession, is a very good thing.

At this point, it is still esoteric enough that I spend far too much time trying to do things that ought to be simple. But things are improving, and the barriers to entry are far lower than they were just a few years ago. I imagine that there is some level of sophistication, when computers are finally programmable by anyone who can describe in a fairly logical fashion what it is that they want done. Everything that we have seen up to this point is prelude to the creative explosion that will occur on that day.

Simple Truths

2008-09-28T23:53:00.002-04:00

Then the Gods of the Market tumbled, and their smooth-tongued wizards withdrew,

And the hearts of the meanest were humbled and began to believe it was true

That All is not Gold that Glitters, and Two and Two make Four –

And the Gods of the Copybook Headings limped up to explain it once more
-Rudyard Kipling

Too many people will look on the current financial crisis and see only the opportunity to pillory their political rivals. Government will be cast as the savior and the villain, and the same roles will be handed to free enterprise. In a world where government-chartered entities (I'm looking at you, Fannie and Freddie) and private banks were forced by law to make senseless loans that they subsequently packaged into securities (now there's an oxymoron that burns), separating the market from the government is both dizzying and unprofitable. A pox on both houses, as well as the recognition that they are both vital.

Copybooks were a device used in years past to teach children, where they would copy lines of text or facts that they were meant to learn and internalize. They might be as simple as methods for learning the ABC's (one I remember that made an impression on me was the entry for 'X' in a copybook: Xerxes did die, and so must I. No varnishing of the facts for the kiddies in the olden days...). They could be Latin or Greek maxims. The idea was that there were important lessons to learn, and you could learn them (along with penmanship, I guess) by copying them.

This is not the kind of educational milieu we live in today, and I'm not suggesting that we should go back to rote, drill, and copying. At least not altogether.

Still, like the Kipling fragment suggests, times of crises remind us that there are iron laws: 2+2=4, and anyone who says otherwise is not your friend, but a devil.

Anyone who suggests that it is a good idea to loan money to people who aren't likely to be able to pay it back- whether it is Barney Frank, with his bleeding heart outraged that poor people are not having their "credit needs" met, or some pin-striper from Bear Lehman CitiStanley rubbing his hands together thinking up ways to pass that trash as a legitimate place for grandma to put her life's savings- needs to review the copybooks.

There really are good and bad ideas that are simple enough to teach children. Prudence really is a virtue, and greed really is a vice. That the largest economy in the world could be brought to a near standstill by liberals and conservatives colluding to ignore simple truths is tragic, comic, and unforgivable.

Fluid Mechanics

2008-08-27T22:00:00.003-04:00

As a chemist, I make stuff. I spend a lot of time thinking about how the structure of the molecules that I make will affect the way the behavior of the material made from the molecule, and what sort of properties I can expect to see.

What I find, now that I am practicing in the real world, is that my intuition about individual molecules is pretty solid. Likewise, my understanding of how to make things was well-formed by my education. There is a great void, however, in my understanding of the mechanics of materials. This is a deep, complex, and mathematically forbidding subject, even for someone with a love and affinity for math. It is a world inhabited by tensors and coordinate transforms and, often as not, nonlinearities that make solution of problems impossible without computational firepower that represents yet another subject I have to master.

This is especially true of the subjects of rheology and fluid mechanics. I am not at liberty to explain why, but I have been intensely concerned with these subjects recently. Learning what I need to know has not come easily. With constant exposure to instrumental analysis of these properties, coupled with as vigorous an attack on the theory and mathematics as I can possibly mount with the constraints on my time and mental capacity, I am just beginning to appreciate what an incredibly beautiful and fascinating world I have been surrounded by, yet been insensible toward.

I found an interesting video about fluid behavior that I want to share. The science is cool, the pictures beautiful, and even the dreamy music sort of captures the wonder of the soft matter world that I am fortunate enough to get to explore.

Future Shock

2008-08-24T14:48:00.003-04:00

I graduated from high school in 1982. Computers had really just begun their meteoric rise to domination of our work, leisure, and culture.

This is a photograph from my senior yearbook. The computers here are the Commodore PET, certainly a step up from the ubiquitous TRS-80 that I first programmed, but not quite as clever as the Apple II. We learned about programming from a fireplug of a guy, a retired engineer whose name I do not recall. He taught "Computer Math" and physics, but I remember him best for revealing the existence of "machine language", the real ultimate language that the computer spoke. All of our BASIC programs had to be turned into machine language to be executed by the computer. This one idea has fascinated me ever since.

In those days, obviously, the idea that you could look at content, with typesetting and pictures and links to other stuff, that was made on one person's computer and hosted on yet another, was the stuff of science fiction at best. To us, who were there when modern computing began, software was not the focus that it is now, largely because there was very little. As a result, there was a drive to understand what was happening down at the metal and silicon that dominated a lot of computer junkies.

The best analogy I can think of is neurobiology. In those days, we had the equivalent of leeches and slugs for computers, so the fun part was knowing what every neuron did. Now, I think we are more or less at the rodent or lemur stage, so we can ignore the lower levels; to some extent, it is counter-productive to think about the lower levels too much now that there are stable paradigms for hiding the details. The details have to be obsessed over by someone, of course, but the real leverage is at the cutting edge of things like distributed processing, web programming, grid computing, and integration of various services like mobile and internet, and the creation of services that live on this stable base that has been built over the last 26 years.

Sometimes, I try to look at the desktop on my iMac with the same eyes that stared at the white on black text and block graphics of the PET all those years ago. I knew then that things would get wildly better- I could see by analogy to other technology like television and radio and so on that we were at the horse-and-buggy stage of computing. But I am still amazed at what it has become, and realize that we have only begun to plumb the potential of the technology we already have, let alone what will come next. Living in a time of near exponential technological expansion makes prediction difficult, but I'm willing to be optimistic and bet that it will be good.

So that's why I always liked Batman the best...

2008-07-26T15:08:00.003-04:00

...Because he's a libertarian hero.

Unlike Superman, who often seems to waste his immense powers on relatively minor villains, Batman/Bruce Wayne pays attention to the importance of opportunity costs. For example, he goes after the bigwigs of Gotham organized crime, not the smalltime petty thieves. He consistently attacks the most powerful villains he can realistically take on with the resources available to him.

The Batman story is also an interesting quasi-libertarian commentary on the shortcomings of government. Like the Mafia portrayed in The Godfather, the necessity for Batman's sometimes dubious methods arises because of the government's failure to protect people and their property against predation. This point is effectively emphasized in both The Dark Knight and Batman Begins. In that respect, Batman is similar to The Godfather in conveying skepticism about government, its motives, and its ability to effectively fulfill even the core "minimal state" function of protecting the public against violent crime.

In two important respects, Batman's message is actually more libertarian than that of The Godfather. While the latter portrays private protection firms (such as the Mafia) as being basically similar to government in their predatory nature, Batman's crimefighting activities are depicted as being both more noble and more effective than those of the generally incompetent and corrupt Gotham authorities.

This quotation is lifted from the generally excellent Volokh Conspiracy, a legal/political blog with refreshingly libertarian leanings.

So...

Have you ever noticed that Hayek looks a lot like Alfred, Bruce Wayne's butler?

I always figured Alfred must be the brains of the operation. If Hayek is Alfred, there's no doubt.

(If you can't be bothered to figure out anything else about Hayek, look up his analysis of the Calculation Problem that dooms attempts to decide what ought to be produced or what "fair" prices really should be. Despite modern defenses of socialism, I still think that this is the fatal flaw, and also a big reason why anything other than modest social welfare programs go quickly to Hell. Or better yet, the road to Hell is necessarily paved with good intentions coupled with unforseen consequences and inadequate data.)

Arctic Melting

2008-07-24T23:19:00.006-04:00

My Dad and I were discussing whether the North Pole would be ice-free this year. Both of us felt pretty certain of our position, but the farther I looked into it, the more complex the issue became. Dad thought he might have actually seen photos or news footage of an already clear pole. For totally different reasons, I had just looked at satellite photos of the pole.

National Geographic ran this photo in June, alongside a story about an ice-free pole:

This is not the North Pole, it is Spitsbergen (at 78N latitude, it is arctic. But not the pole.) Worse, the photo is listed as undated. It isn't necessarily deliberately misleading, but I was misled by it. And the original story did not have a caption on this photo. So it looked like the "North Pole" was already ice-free.

A NOAA satellite photo from earlier in July shows that there is ice:

The ice is there, but it is thinning, and there are apparently credible predictions that there might be an ice-free pole by 2011-2013 for "the first time in history" (Really? Who was looking until recently?)

These are, however, projections. I do not mean to deride projections, but they do need to be properly discounted. Earlier this year, there were predictions that this year would see less arctic sea ice than last year, if the prevailing trend continued. However, it did not:

On the one hand, the extent of ice is below the 20 year average line. On the other, what is so special about those 20 years, and in any case, the claim that will be falsified or vindicated is whether this year will be a)ice-free and/or b) of lesser extent than last year. I am not nit-picking, but I do want to keep our eyes on the prize. It is great when one can get a clear answer, and all too uncommon, so however things turn out, it is cause for excitement.

Am I 'cherry-picking' data to 'disprove' global warming? No, a thousand times! I just am not going to pretend that every piece of data lines up perfectly, or that this is the first time anyone ever thought of such a horrible thing as an ice-free pole. I think it is inexcusable to tell less than the whole truth when so much is at stake, both environmentally and socially.

Take a look at this New York Times page:

I'm sorry it isn't more legible, but you can see that there was at least some worry about an ice-free North Pole in this story from 1969.

The current concerns, nor those in the mid-60's, are not the only times there was worry about global warming. In the 1930's, just before the Dust Bowl, there was concern, and that concern seemed to be borne out by the drought. Later there was cooling, and while there was no where near the scientific activity or 'consensus', by the 1970's there were worries of an ice age.

Climate is complex. Some of the most touted models of catastrophic warming are derived from tree-ring data which is notoriously bad as temperature proxies. Notorious for being affected by things other than temperature (e.g rainfall, condition of bark). Notorious for being incomplete and poorly archived, and notorious for not being kept up to date. Some dendrochronologists are becoming notorious for not revealing their data or methods properly, which is, and should be, alarming, whether it is nefarious or merely contrary.

The science is being done, and generally by good and competent scientists, I believe. But do not listen to the refrain that "The science is settled". The science is never settled. Newton's laws ruled for centuries before being revised by Einstein. Why should climatology be above reproach?

Beware of Scientists

2008-07-20T02:20:00.002-04:00

In Eisenhower's farewell address, there is a line that has become iconic, a warning of what the technological powerhouse that is the US economy that helped win WWII could become:

In the councils of government, we must guard against the acquisition of unwarranted influence, whether sought or unsought, by the military-industrial complex.

Again and again this phrase is invoked, tarring (with justification aplenty) the defense industry and the business of warcraft.

Another line, mostly forgotten, chills me to my core as a scientist:

...in holding scientific research and discovery in respect, as we should, we must also be alert to the equal and opposite danger that public policy could itself become the captive of a scientific-technological elite.

Ike hit the nail on the head.

There are great dangers when scientists become activists. One is that activism is far easier, and often more socially rewarding than science, and so becomes an end in itself, pushing the science to the rear, ironically betraying the only real reason anyone would have to listen to a scientist.

Another is that advocacy requires taking a stand in a political framework. Reversing oneself is damned near impossible in this context. Scientists, no matter how hard-headed, or committed to a scientific position they become, are always expected to defer to new data. But politically, any wavering diminishes one's rhetorical and persuasive currency, and must be avoided, whatever the contradictions. This is also deadly to science.

Finally (and by finally, I only mean for the purposes of this post. One can go on and on with reasons why activism poisons science), activism by a scientist implies something utterly illogical in many cases- namely, that knowing what is happening implies that one is competent to judge whether it is good, bad or indifferent, and that once this judgment is made, that the activist has any clue what to do about the situation.

Scientists tend to be fascists, in a limited sense of the term. I know this statement might irk the hell out of many of my friends that strive for liberal political enlightenment and social justice. But many of the good people in science that I know would not think twice about taking away any manner of freedom or choice when they believe that the scientific evidence suggests a best course of action. Some have been bold enough to say, in front of God and everybody, that it is important to know when to favor effectiveness over accuracy, if the cause is urgent and noble.

I think about the eugenics movement. Once the Nazis discredited the idea, it was conveniently forgotten that many of the leading scientific and intellectual lights of the early 20th century were strong advocates for sterilization of 'undesirables', including minorities. They had the data, the models, and the best interests of everyone at heart. And they were being scientific. Who could oppose that?

Science is the best tool we have for understanding stuff. But it is inadequate to the task of deciding what the stuff, or the understanding of it, means.

My Bro

2008-07-03T11:54:00.003-04:00

My brother is willing to make a fool of himself for the good of children. This makes him a hero to me.

I have posted a few things on this site, and plenty elsewhere, that sits me squarely in the agnostic-with-Christian-culture camp. I am not apologizing, nor proselytizing. It is the truth, and I'm not able, by an act of will, to either become a dyed-in-the-wool uber-atheist or a washed-in-the-blood believer. I am what I am. I find Richard Dawkins and the other militant atheists noisome and surprisingly unmoved by what seems to me to be deep human psychology. At the same time, I think a lot of conservative/fundamentalist Christians are scared shitless of science, and support abominations like the Creation Museum and Intelligent Design, much to the weakening of their claim of any intellectual honesty.

My brother is a minister, focusing on elementary school age children, at a fairly large non-denominational Christian church. I doubt we would see eye-to-eye on matters like doctrine or faith. But despite my misgivings about the ontological foundations of religion, as a practical matter, I can appreciate when things do good, rather than evil. And his work falls into decidedly into the realm of good.

He brings the love of God to little kids. I say this without irony; while I might doubt the soundness of the foundational premises of the statement, the fact is that the schema is deeply part of our culture and psychology, and is capable of helping children grow up to be decent and good human beings.

The immediate counter is that he is filling their minds with nonsense for which no evidence exists. But I would disagree, no matter how thoroughly convinced I might become that the empirical basis of Christianity is lacking. Because I know that my brother is steady, and kind, and reasonable, slow to judge, and quick to reach out in friendship, a voice of wisdom at a time children very much need to hear one. Most children will receive some sort of religious training. At my brother's hands, their example is one of hard work, and sacrifice, goodness, and temperance. Not only do I think he is providing a good example, that I hope his young charges will grow up to follow, but I also see him as inoculating them against extreme strains of Christianity later.

I have argued before that the desire to eradicate religion is foolish and quixotic and doomed to utter failure. Since religion is going to exist, I hope for, and support people like "Mr. Dan" (as the children call him) in what he is doing, whether I understand or believe in all of it or not.

Chemistry

2008-06-29T23:29:00.002-04:00

I am one of the luckiest people walking this Earth. I have a great family, and live in the land of plenty. I could rhapsodize about my wonderful wife and beautiful sons, but this is not the venue for that. I'll focus on my professional life, because there, I am also fortunate beyond reason. I am a scientist, but even more, I am a chemist.

I started my scientific life in physics, and I have stayed pretty connected to that world. Still, I think that chemistry is more interesting than much of modern physics because chemistry deals with processes and materials that one is able to experience. With 'stuff'. With things that happen at a scale that we can care about. Solid-state physics is kind of like that, so I sort of adopt it into chemistry...

I think some people are beguiled by time travel, or exotic states of matter, or that the equations that 'explain' the universe may someday fit on a t-shirt. This stuff is fine, as far as it goes.

I find things like silly putty, liquid nitrogen and epoxy every bit as fascinating as anything I could learn from the Large Hadron Collider, because while they seem mundane, something very fundamental and surprising is really at the heart of them.

Of course a billion gazillion dollars worth of physics hardware is going to tell you something interesting. But so will 5o cents worth of silicone polymer if you know what to ask of it. Neither one is likely to lead directly to something useful. Both are deep. Saying that you are probing the heart of matter sounds more important than playing with silly putty. But I am not convinced that they are necessarily different, depending on the approach taken.

I believe that the natural world is predictable to some extent, but that it is too complex to predict much in any detail. A bias towards trying things is the only thing I can see that is likely to work to help solve problems. Knowing what holds nuclei together is important, and I want the LHC to help figure out all those kind of physics-y things. Yet I wouldn't oversell what knowing this will get us. I doubt that knowing things at a super low level 'ends' science, or that physics is somehow the most fundamental science, whatever that is supposed to mean. Details are important, and stuff emerges that cannot be predicted, even in principle, I think. We once thought that there was a hierarchy of knowledge, but that seems pretty vacuous now.

Physics can be pretty precise when talking about certain simple things. My sense is that the precision and mathematization of physics is misperceived as a plus, though- fundamentally the deal made in physics is a trading off of relevance, detail and usefulness for tractability. To the extent that experimentation becomes something to support theorizing both theory and experiment have become perverse.

I hope it isn't too unkind to draw an analogy between modern physics and economics- we are far into the realm of diminishing returns with respect to particle physics. With chemistry, we are just getting started. There are huge swaths of the periodic table yet to explore.

I have no beef with big physics. String theory is not going to make the periodic table change, though. It may or may not lead to a theory of everything. Chemistry certainly will not. But I'm not apologizing for finding chemistry far more compelling. I want the physics to happen. But I am content to read about it in the newspaper. Chemistry, on the other hand, I want to do.

Perhaps my biases come from the fact that chemistry is just too complex for theory to handle. No chemical reaction worth doing is going to be amenable to exact calculation for a long, long time, and even then, I predict that the results would be far less useful than just running the reaction. I am not, in any fashion, knocking the efforts to try. There is a lot to learn, even without doing reactions. Less than by doing them, I'd wager, but still.

The Shock of Recognition

2008-05-23T22:17:00.003-04:00

I can't hide my suspicions any longer. My father has been leading a secret triple life as diplomat, oatmeal/diabetes spokesman, and debonair, charming Southern raconteur.

Emergency!

2008-05-12T20:37:00.002-04:00

This is almost a perfect superposition of cool and nerdy. I love it. It is crying out to be done again and again with the stakes getting progressively higher. We'll have to stop, of course, when someone puts their eye out, but until then, it should be awesome.

Emergency Party Button. Yes.

Я пришел, чтобы мужчина растительное

2008-04-28T00:14:00.002-04:00

My Russian is horrible. I supposedly took a couple of years in college. There is only the barest residuum of any of it in my mind. It was a requirement for graduation, which was the only reason I spent any time at all in the classes, which were GPA busters for me. I have very good friends from that era, all of whom were quite fluent and literate in Russian. I am a foreign language moron.

The title is a stupid inside joke several of us shared in college. We measured fluency in a foreign language by how well the speaker could translate one dumb phrase: "I have come to see the vegetable man." I forget the origin of the phrase- it might be a Monty Python quote, or it might have sprung from a bottle of cheap wine we shared.

As I age, and come to grips with the fact that I am mortal, finite, and have all sorts of limitations, my inability to process foreign language stands as typical of things I absolutely suck at. I put no time in to them unless forced. I become dyslexic and twitchy when I try to study them. I am petulant when I have to face them.

I think it might be that I just don't like things that don't seem logical to me. This is perhaps a reason why I gravitated to science. I'm not proud of the blind spots that I have, and I know that in some way, it is something that will always be hidden from me. This pings my curiosity, and makes me sad that I haven't mastered myself more.

Why liberal sensibilities turned me Libertarian

2008-04-27T21:36:00.002-04:00

I take no end of abuse for saying I am libertarian. Libertarians are the ones that believe that the police and federal highways should be private, remember? And they are just closet republicans that want to smoke dope. And they magically believe that the free market will solve everything. And libertarians don't want to help anybody. So I must be an asshole.

Well, I'll cop to the asshole part, but none of rest of the above is true for this particular libertarian. So I will offer a small apologia.

I'll make it quick, because my conservative and liberal friends will soon drown me out with their incessant squawking about how evil I am.

I don't think that everything can be private. Incentives matter, and there are lots of times when the incentives would be all wrong for private ownership. No one should own the air. Highways can be made private successfully, but in general, there is a sort of monopoly relationship that gets established that isn't healthy.

The legitimate initiation of force needs to be confined to someone at least sort of beholden to everyone. The perverse incentives here are probably obvious. Private security and military operations have their place (I live in the hometown of the founder of Blackwater. Whatever you think of their performance in Iraq, they have a track record of success overall. Yes, they slightly give me the oogies. But so do exterminators.)

My argument can be distilled to a salient example that illustrates my general feelings, which are that if it is ethical, possible and practical to keep things out of the hands of government, then it should be left to individuals. There is a lot of room for debate. That's fine. I welcome it. But this lets you know from where I start, and what sort of convincing you'd have to do to overcome my bedrock assumptions.

Biofuels are in the news. They are helping starve the third world. Yet, they are almost entirely the project of governments that are trying to do environmental good. Pressure was applied from many quarters for the government to mandate biofuels, irrespective of the fact that many economists could see, and verily shouted from the rooftops, that this would create food shortages. The reliably 'progressive' newspaper, the Independent in London (I'm picking on a British paper because I can't mention a domestic news source that right and left won't declare as in the tank for the other side) said in 2005

"At last, some refreshing signs of intelligent thinking on climate change are coming out of Whitehall. The Environment minister, Elliot Morley, reveals today in an interview with this newspaper that the Government is drawing up plans to impose a 'biofuel obligation' on oil companies ... . This has the potential to be the biggest green innovation in the British petrol market since the introduction of unleaded petrol."

Imposing a biofuel obligation was the only way the market would respond. Biofuels do not make economic sense. I'm not going to argue with you- they don't, or they would be pursued in the absence of subsidies. Now, there can be other reasons to do things that are uneconomic, but the environmental argument doesn't hold up well, either. The same newspaper said last week:

"The production of biofuel is devastating huge swaths of the world's environment. So why on Earth is the government forcing us to use more of it?"

I cribbed this observation from Mark Steyn, but even if he were the devil, the damnation comes from their own history. The environmental degradation the Independent decried is not half the problem. The incentives provided for biofuel have incentivized food right out of starving people's mouths.

This bothers me. I do have a heart. I care about people, and I care about the earth. I just think that government, despite its best intentions, ends up making things worse much of the time. Other times, the intentions are not good, and are the raw exercise of power to curry favor. Not everything can be left to the free market (of ideas, as much as money). But given the unresponsiveness of government, and the lack of feedback to dissuade them from disastrous policies (yes, I am thinking of the War on Drugs, despite not partaking myself), having economic chains to yank can give us all more power than ceding all our power to government.

Springtime

2008-04-23T21:48:00.002-04:00

Spring has finally sprung, more or less, in the frozen steppes that make up West Michigan. It is rumored that a minor cold snap is coming, but we have had mid 70 degree weather for the last few days. It has been glorious.

My older son, my 11-year-old, spent hours this afternoon jumping on a neighbor's trampoline. Super fun. We are lucky to have a handful of good-natured neighborhood kids for him to run with.

I was watching, thinking about how his life is so different from how mine was at his age. The trampoline was completely encircled in a protective net. The net is a decent metaphor for how protected his life has been. A metaphor for my childhood would have been laughing kids on a rusted out sliding board with a wasp nest underneath.

We have been very careful with my son. He didn't come to us easily. We struggled with miscarriages and tubal pregnancies and all the heartbreak anyone should have to stand trying to love someone into existence. We had just about given up when he was conceived. We were worried the entire time my wife carried him. Surprisingly, the pregnancy was nearly perfect, as was his birth. He has been a hardy, cheerful and robust child. Tonsillitis got him down sporadically for a few months a couple of years ago, but when the tonsils were gone, he went back to being hale and fit. He has been sick few enough times to count on fingers.

But he doesn't get out much. He gets outside with friends, but he has never willfully done anything I would consider dangerous. He has never stung by a honeybee by trying to catch it (though he did get nailed by a yellowjacket while he was minding his own business). I am certain that by 11 I had been stung at least 11 times by honeybees, trying to put them in jars, or catch them by the wings (which you can do if you are really careful), or by stepping on them. I had friends that deliberately stirred up bees, as sort of a man-vs-nature contest. The combatants included their parents, too. I grew up around fun, crazy, risk-loving nuts.

My son hasn't had stitches or ripped out a scar, or had a bike crash, or had to get a tetanus shot from stepping on something. I, amazingly, did not break any bones other than toes, so we're almost even there. But lordy, I tried.

No, this child has always been prudent. Not cowardly, but brave in a prepared and sober way. Very reasonable, honest, and very principled. I am very proud, even as I marvel at him.

Our second child is 2 at the moment. We had plenty of heartache and trouble on the way to him, too. Like his brother, his gestation was without incident, as was his birth. And so far, he has been hale and hardy.

But this one is also very different from his brother. He is recklessly curious, willing to take physical risks to get in or onto something. He is not showing signs of his brother's willingness to be reasonable or careful. He appears to be trying to learn something most of the time, but is very impatient and moody. He is delightful. Even, if not especially, when he is being stubborn. He's tough and hardheaded, and laughs a lot. He shares those qualities with his whole family. I don't think he'll tolerate us trying to protect him like we did his older brother.

The best part of fatherhood in my eyes is getting to lead these youngsters out into the world and help them poke at it, and learn about it. They are restlessly curious, even the more serene of the two, which is something we can share.

Tilting at Windmills

2008-03-08T00:39:00.002-05:00

Windmills are a favorite of the granola and birkenstock posse, but they are really a sort of stupid idea except as a tertiary, supplemental form of power. Sometimes, the wind doesn't blow. Sometimes, it blows too much:

Am I the only one creeped out by the BP ads, where some idiot man- or woman-in-the-street gives their half-assed opinion about where we ought to get power? Some yutz talks about how great solar power is. It is also a good supplemental supply, but right now, solar's contribution to powering the world is best measured in parts-per-million.

I recognize that oil is a finite resource (though it is routinely underestimated), but I also know that the solution isn't some goddammed oil company feeding off subsidies while they pretend to create the next energy source. And it sure as hell isn't like they are really listening to some yokel in his porch swing opine about energy economics. Beyond Petroleum, my ass. The sunshine these bastards are trying to pump up our skirts isn't going to drive a solar grid.

I don't like being patronized. Just pump the oil out of the fucking ground, BP. Soon enough, the forces of supply and demand will knock you off your high horse unless we are bamboozled into giving you even more tax money to keep us under your thumb.

Home Sweet Home

2008-03-04T22:08:00.003-05:00

I've been following election returns tonight. I don't really care about the outcome as much as I enjoy the spectacle. It's like some sort of extremely perverted sport.

While checking the news items, I came across this photo of Earth and its moon, taken from the Mars Reconnaissance Orbiter back in October of last year.

If you look really closely, you can see Hillary, Obama, and McCain gathering lawyers in to corrals for the election this fall.

Actually, it is comforting to see how all our political chicanery is invisible from an interplanetary perspective.

A thousand years from now, people won't remember Barak Obama, or Hillary Clinton, or John McCain, unless you count ancient history scholars. But they will remember that this was the age when we left Earth to visit the moon and planets. Whether they look back on this as a golden age, or hopelessly primitive, I'll never know. But assuming both humanity and history still exists, this will be noted as the time when we first looked on the face of other worlds, and on our own from that perspective.

When people sneer at the accomplishments of the space program, and stomp their feet and demand that the resources would be better spent here on Earth, I take a great deal of unholy pleasure in thinking that I don't know the names of any of the critics of Galileo, or Columbus, or the Wright Brothers. None. I suspect the verdict of history will be similar for the small minds that insist that we stay here, where we 'belong', and forgo exploration to hew to whatever doctrine they count as important.

Frank

2008-03-03T21:26:00.001-05:00

more confident
Originally uploaded by sciencedave

This is Frank, also called Frankie. Short for Francis. I was sort of hoping to name him Brak, but was overruled.

He is our fourth and (oh please, God) our last cat for a while. He is very relaxed. Our tabby wanted to push him around the first few days, but he finally took up for himself, and everything is now fine. Lucy (the tabby) will hiss at him once in a while, but he's a good bit bigger than she is, and now that he has shown that he will defend himself, it's all bluster on her part.

As a scientist, I am drawn to cats because they are very complex and intelligent, but unlike dogs, they haven't been molded to do our will. They do what they do with minimal perturbation caused by any expectations we humans have for them. I admire that.

Three years

2008-02-28T22:51:00.002-05:00

I just realized that as of the 23rd of this month, I had been blogging for 3 years. Three, coincidentally, is also the number of people who read this blog. Counting me.

Something cool: a movie of an electron riding a light wave.

A short blurb that (barely) explains what you see in the movie is here.

Something that I find really interesting is that the durations of light pulses used to make this are shorter than the time it would take an electron to (classically) circle the nucleus in a hydrogen atom. Attoseconds are 10^-18seconds. I haven't checked the math, but I think that I read that an attosecond is to a second as a second is to the age of the universe. It makes 3 years of blogging seem kind of inconsequential, really.

Wild-eyed Southern Boys

2008-02-28T21:50:00.002-05:00

Living up here in the Great White North, I get a little ribbing about being from Kentucky, like I grew up without shoes, minding a 'shine still, shooting possums and kissing my cousins. I take it with a smile, mostly, because I frankly know that my tormentors are full of shit. There are things that get under my skin a bit, though.

1. References to the movie 'Deliverance'. First of all, Goddammit, that was in Georgia. Not that Kentucky doesn't have plenty of rednecks, but I once say a traffic dustup in Macon, Georgia, boil down to a guy with a machete vs a guy with a gun. Over who got to the light first. You would never see that kind of nonsense where I come from. In Kentucky, no one would have wasted any time with a machete.

I'm not all that offended by the implication that the south is full of violent, inbred, familial idiots. I was menaced by one with a logging chain who lived down the street from me when I was 6 years old. (Archie. Damn.)

No, what pisses me off is that the 'heroes' in Deliverance escaped. It just isn't realistic.

See, I grew up in a home where my father was a lifelong Democrat, and who was pro gun control. And we had a 20 gauge, a .22 and a .38 in the house. I had a BB gun or two by my 10th birthday, and was deadeye before I ever fired a real weapon. I am cross-eyed, near-sighted in one eye and far-sighted in the other, and have to shoot left-handed because my right eye sucks. And I can still hit a bullseye at 500 meters. To say that guns are part of Kentucky culture is to say the sky is blue.

Most of my buds growing up could drop a buck at 400 yds while finishing a six-pack. No dipshit with a crossbow and a canoe would make it out alive, 'kay?

2. People talk about moonshine like it's bad. While there is such thing as bad moonshine, bootlegging was a typical Scotch-Irish response to poverty. Make money, fuck the law, and invent NASCAR in the bargain. These people had been maltreated at the hands of government for hundreds of years before ever coming to the New World, so fine points like legality barely registered. They figured no man had any right to get in between two others who were peacefully going about their own business. Now, most people I know who were involved with moonshining had no respect for assholes who made popskull. But the driving of this business underground made the profit high enough that standards slipped.

Rumor has it that someone very close to me was raised by a woman married to a moonshiner. I won't name names, but she knows who she is. (Hi, Mom!)

3. Shoes. I always had shoes. There is a big difference further South, where it might be practical to not wear shoes most of the year. And I went barefoot a lot in the summer, but not because I didn't have shoes. Kentucky is not Tennessee.

4. Stupidity. Listen, I know that there are lots of ignorant people in Kentucky. Some damned proud of it. But some of these same people are resourceful and crafty and shrewd, and like nothing better than to shuck some arrogant Yankee out of his money. Kentuckians are contrary, fierce, loyal, profane, tough, and clever. I am proud of who I am, and of the people I belong to. I sure as hell won't disown my great heritage just because now I'm all 'educated', and If I had any cousins worth kissing, I might. What's it to you, anyway?

So, yuck it up, Yankees. Just be careful when you go out in the woods, even with your crossbow.

I hate politics

2008-02-20T17:23:00.002-05:00

"Barack Obama will require you to work. He is going to demand that you shed your cynicism. That you put down your divisions. That you come out of your isolation, that you move out of your comfort zones. That you push yourselves to be better. And that you engage. Barack will never allow you to go back to your lives as usual, uninvolved, uninformed."

"You have to stay at the seat at the table of democracy with a man like Barack Obama not just on Tuesday but in a year from now, in four years from now, in eights years from now, you will have to be engaged."

These two statements by Michelle Obama at a rally at UCLA recently stopped me in my tracks.

I am pretty libertarian in my outlook. Small "l", but a big believer in leaving people to find their own bliss, and to not presume that individuals or groups, including governments or corporations or churches know better. They can help, but should not prescribe, often even for the "greater good", since this is a road too often paved with good intentions that leads to...ah, screw it. I'm not going to bother justifying being libertarian. I just don't trust the government or the corporations to act on my behalf. Sorry.

All that said, I was beginning to be a bit beguiled by the 'Audacity of Hope." I think Obama is one of the most interesting (and hypnotic) political figures I ever remember seeing.

But, as God (whether S/He exists or not) as my witness, neither Obama nor Hillary nor St. Ronald Reagan will ever take my cynicism from me. I will stand in outright rebellion against any foe, foreign or domestic, that tries to make me give a damn, or to work for, anyone else's idea of political rectitude. No way.

All kidding aside, this kind of talk bugs me. I don't like spiritual spirituality, let alone equating politics with some sort of moral imperative. No. No. NO. I will not engage unless I want to. I will not work for Obama or any other human being unless I find common cause with them. I will not bow to my government. No.

Maybe this was just high-minded political fluff talk. I don't disagree with a direction of being hopeful and working together. I think we should. But when maybe 1st lady starts telling me what I am going to have to do, I may have to resist.

Workers of the World, Untie!

2008-02-16T23:23:00.003-05:00

(Yes, the misspelling is deliberate. Sheesh.)

I was thinking about a something someone recently opined about the theory of relativity, and I began to wonder- when will there be 'proletarian' discoveries in pure physics again, if ever?

Think about radio, TV, internet, power generation- all these things that are at the center of our culture. The bulk of enabling technology flows from Maxwell's equations. Beautiful and deep, they are simultaneously immanently practical, and have made a huge impact in the lives of most people on earth.

Chemistry is proletarian to the point of being ignored- it is so useful and productive that it falls into the background. I'm never at a loss to explain to someone who is skeptical of science all the good modern chemistry can do for them. The guy/gal on the street hates chemicals, but they love new fragrances, paints, dyes, drugs, fuels, fabrics, etc.

As much as it pains me to admit it, biology is clearly on the earliest edge of a exponential explosion of relevance to the welfare of humankind. Chemistry will be focal to this, no doubt. Some biophysics might be central, but I am pretty ignorant of where this is relevant to the current biotechnological program.

Solid state physics certainly changed the world, but that has been handed off to engineers and materials chemists for a long time. High Tc superconductors? Hmm.

What has fundamental physics done for me lately? MRI, maybe? Maxwell and Schrodinger plus engineering. I'm not saying that physics cannot, or will not, be the cornucopia of future technological blessings for us all. I'm just wondering whether anything at the forefront of physics is likely to do much anytime soon. I'd be happy for someone to rebuke me and point out all that is just around the corner, but I'm not seeing it. I ask as an unrepentant physicsphile. I don't really believe in nanotechnology yet, and most of what I see will be chemistry. I wonder...

Parenting

2008-02-16T18:18:00.002-05:00

I have two boys, separated by 10 years. My older boy is a joy, well-behaved and smart as a whip. My two-year-old is a barrel of fun, too.

The best things I have experienced as a dad have revolved around seeing my children figure something out. When Sam, my elder son, figured out geometric congruence on his own recently, I was quite proud. When he was dissed on an online combat game by a bunch of kids in their late teens, he set booby traps for them and sniped some of the others. They have taken to asking him his opinion on how to do things.

The emergence of language with Sam was great fun. Charlie is just at the beginning of this right now. We have been teaching him animal sounds. He is quick to make the sound of any animal he sees, and will name an animal if he hears the sound. The acquisition of this has been very recent, and was pretty abrupt. Surely, he must have been piecing thing together, but its emergence as behavior has just in the past week or so, and it is very consistent.

We were playing, and he knocked over an end table that I have that has a built-in lamp. He thought this was great fun, and climbed on it. I wanted to right it, so I said, in a somewhat stern voice, "Move. Move!". To which he grinned widely and responded with "Cow!"

Reasoning comes more slowly, but I always push it, asking questions that I know that they cannot answer, mainly to get them in the habit of asking question, and to let them realize that answers exist. Years ago, I was playing with Sam with a helium balloon. I asked him what he thought made it 'fly'. He said, "I dunno, Daddy. What?" I expected the conversation to go back and forth. He was far too young to understand buoyancy, but I still think talking back and forth is great exercise for a child's mind. Even as an adult, I often hear explanations that I don't understand, but that I still keep deep in my head, and when I figure out enough, suddenly it makes sense.

I said, "Well, there is something inside the balloon that makes it go up into the air. What do you think is inside?" Sam thought for maybe two seconds, and said "Birds."

Weird

2008-02-15T22:49:00.003-05:00

I love xtcd.

I spend a lot of time thinking about chemistry and physics. I have had lots and lots of school and lab time, and I'm lucky to do science for a living.

But there are lots of things that I still find mysterious and weird. Magnets and gyroscope do things that seem completely magical to me. Yes, I've done the math. I barely apprehend the fact that conservation of angular momentum stems from the rotational symmetry of space, and I have worked through the basic relativity to see that magnetism is sort of a consequence of this. I know lanthanides are contracted due to relativistic effects.

Still...

Somehow, a magnet rotating downtown makes my lights shine and my computer run. Yes, yes, magnetic induction, Maxwell's equations. Very nice. So why? Why do the electrons in my lamp give a shit what the big magnet downtown is doing? Knowing the math is not the same as knowing the reason. It's deep, and mysterious, and yet so ubiquitous that it is easy to ignore. My lamp ignores the movements of paired electrons. But not those that are unpaired and aligned. I am happy to use electricity, and I feel especially fortunate to have been schooled in physics as an undergraduate. But I am still not satisfied. I don't care if the universe has 3 dimensions or 21. I want to really, really know why my gyroscope doesn't fall over, and why magnets stick to my refrigerator. So I keep poking at physics and mathematics long after my mental prime, hoping I'll get it someday.

Lately I've been playing around with symmetry and Lie (pronounced 'Lee') groups. Symmetry has deep connections with physics, as I alluded to above. Chemists get just a little taste of symmetry and group theory, when they learn how to use point groups to predict the bonding and spectral characteristics of molecules, usually in an inorganic chemistry course. The presentation is usually abysmal, with no foundational theory, and very little motivation. You learn to 'do' group theory without really understanding it. In fairness, it is usually shoehorned into an already filled-to-the-brim survey of all the chemistry not covered in organic, which is, by virtue of the peculiar properties of carbon, pretty unique. If you know only organic chemistry, you still know a lot of what is done in the chemical world.

What I am fiddling with now has little direct connection to chemistry, or at least not that I am able to see. I am looking at it as more of a means of retaining and rebuilding my abstract mathematical skills (since I have forgotten a lot of the analysis and topology I once knew.) What I am interested in doing is tying together a functioning understanding some of the more modern methods of mechanics and field theories (which tend to center a lot on differential geometry). At some level, deep topological symmetry and fields reconnect with statistical mechanics and hence condensed matter physics and chemistry, but I am not sure I'll ever get good enough to see this clearly. I'll be happy to know some of the basic ideas. Every time I've put in serious effort to understand stuff over my head, I get at least something that helps me understand more prosaic stuff, like chemistry...

Perspective

2008-02-12T23:45:00.002-05:00

Look again at that dot. That's here. That's home. That's us. On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives...

Our planet is a lonely speck in the great enveloping cosmic dark. In our obscurity, in all this vastness, there is no hint that help will come from elsewhere to save us from ourselves.
-Carl Sagan

As Voyager looked back toward Earth, as it left the solar system, glare in the optics enveloped the 'pale blue dot' of our planet in what appeared to be a sort of spotlight. But really, there is no spotlight. Just a tiny planet, revolving around an average star, in a typical galaxy. Home, for now, to us.

We may be overheating the planet, and our world may be headed for an ice age. The two aren't mutually exclusive. The plain fact is that we are a recently emergent species, and there is no guarantee how long we'll last. There are misanthropes who chuckle at the thought of humankind's demise, so the dolphins or snaildarters or Ewoks can rule the planet in peace and harmony. But not me. I suspect humans will outlive me by thousands, perhaps 10s of thousands of years. But probably not millions, and that's very likely the kind of time the Earth has in some form that will sustain life.

No one will be here to gloat nor mourn when the last of the pyramids is ground to dust, or when the last vestige of art or architecture crumbles. The death-cult of some treehuggers has them naively imagine themselves there to tell us all "I told you so" as civilization disappears. When the last ocean boils, or freezes solid, or is enveloped in the death-throes of our sun, the passage of this beautiful place will go unrecorded.

So live now. Dance on the pale blue dot while there is time. And fuck anybody who won't.

SHAZAM!

2008-02-12T23:25:00.003-05:00

This can't be good. Jesus is fixing to open a can on Brazil, I'm betting. And we're going to be next.

Hackity Hack

2008-02-01T16:54:00.000-05:00

All three of you who read this may have noticed that I am fond of Java for doing the sort of science-y programming tasks I find necessary to do. I like it because the same code works on both my Mac and my PCs, and because it is reasonably easy to do things using it.

Lately, I have picked up 2 more programming languages, as well as a scripting language. Many popular languages in the programming world are heavily influenced by the C programming language, a system developed by Bell Labs a long time ago. So to some extent, it is just a matter of learning certain dialects and customs peculiar to a given language to be able to use it.

Microsoft has made some of its programming tools available free for downloading. The versions that are free are restricted in certain ways, but are still very powerful. I am not aware of exactly what the restrictions are, but for the kind of noodling I am likely to do, the restrictions might as well not exist. These ‘Express’ editions are available for Visual Basic, Visual C++, and Visual C# (the latter two are, not surprisingly, also variants of C).

Better yet, Microsoft has a handful of bloggers who use these editions to do neat stuff, like control disco dance floors and make cool web sites. They bill this as “Coding4Fun” and aim to involve more experimenter types with programming. Even a rank amateur can find tutorials to get started. I hope lots of people decide to learn to program, if only a little. It makes everything look different, when you can understand a little of the software behind the modern world.

I chose to look at C# (pronounced “See sharp”) for a couple of reasons. First, I am already comfortable with C. Also, C# has been touted as being a lot like Java. I remember from my daze (er, days…) as a physics undergraduate that there was no better way to expose how poorly I understood a problem than to try and work it more than one way. So I hope to solidify my understanding of Java and object-oriented programming with this exercise.

Also, one of my heroes, Johnny Chung Lee, has done some downright incredible things with C#. So I figured it might be fun to follow his lead a bit.

In my next entry, I’ll regale you with the story of how interesting this has been, and how easy it was to do a few things in C# that are, frankly, a major pain in the ass with Java. But for now, let me just say that I am pleased at how well the system works, and the learning curve has been reasonably gentle, largely because Microsoft has support the creation of lots of interesting examples. Microsoft takes some knocks, but this is a good thing that they do, whatever their motives might be.

The other language I am fiddling with is Objective-C. It, too, is ‘object oriented’. However, unlike the other languages I am using, it departs from the more-or-less standard syntax used for passing messages to objects. To make what this means a bit clearer, suppose I have a clock object, and I want to set it with the current time. In Java, or C#, this would look something like this:

Clock myClock=new Clock();
myClock.setTime(now);

First, I declare a variable myClock to be a Clock object, and by using the ‘new’ keywork and the ‘constructor’ Clock(), I tell the computer to do whatever it needs to in order to get myClock set up to run. By using the ‘dot’ format for message passing, in the next line I tell the clock object named myClock that I want to set the time by having it invoke the setTime( ) function, with the parameter ‘now’. I’m obviously glossing over a lot that some of you don’t know. The details don’t matter- the differences will be clear.

In Objective-C, the same task would look like this:

Clock *myClock=[Clock alloc];
[myClock init];
[myClock setTime: now];

There is a little more tinsel on this one, and I have made it slightly more verbose than necessary, since the first and second lines could be put together, and Objective-C actually has a ‘new’ message that can be used in this context. The asterisk is more interesting, though. In C, this is a way that a variable will be used not for a piece of data, exactly, but rather, to hold the address of a piece of data. The first line says “please allocate a piece of memory big enough for a Clock object (details of which would be specified elsewhere in the program), and return to me the address of this block of memory”. The next line says “using the object ‘pointed to’ by the address in myClock, please do a clock initialization, whatever that is”.

I am not merely being flip when I say, “whatever that is”. A point of using object-oriented programming is to be able to use other bits of software that you might not have developed by knowing only what kind of messages it understands. The details can be ignored, forgotten, or set aside for the moment. All the programmer needs to know is what the object wants in the way of messages, and what it will return in data, or other messages.

Now, this same philosophy is at work in Java and C#. My reason for fooling with Objective-C is that the Mac’s operating system is programmed in Objective-C, and it is the foundation of most of the programming resources available on the Mac.

There are details that I find weird in every language, weird things that are hard in one language and easy in another. Moreover, there are features far deeper than what I have alluded to here that make each particularly strong in certain contexts.

I have left most things unsaid. But I hope, by showing little glimpses of code and descriptions of what is going on, I can give an appreciation of some of the inner workings of computer programs. I will follow up with little examples over the next few posts to make this less abstract.

Computers. I hate 'em.

2008-01-28T01:00:00.000-05:00

Not really, of course. They are just kind of frustrating, at whatever level of expertise one might have. My dad is not a newbie, but most of the problems he calls me with are relatively straightforward for me to fix. In my own work, I can find myself chasing a subtle bug in a program, or looking for days for documentation to figure out how to do something that seems like it ought to be easy. And for just about everyone, from rank amateur to the real hardcore programmers I know, there are times when things happen that just defy explanation.

One reason for this is that computers have become complex enough that they can retain a rather long memory of things that are done to them. Murray Gell-Man, a physicist, was recently talking about how the universe is the product of fundamental rules plus a bunch of accidents. (You can find this talk, and plenty more to entrance you, at TED.com. If you like hearing smart people talk about the things they know about, you can waste a lot of time at the TED site.)

It made me think- computers have all sorts of 'accidents' going on all the time. Things happen that perturb the system in ways the programmers did not predict, and probably could not predict, even in principle. Some are obvious bugs- some action a person takes sends the computer to a nonsensical part of memory. Others may be more subtle, where some lack of resources was not imagined, and was never encountered in testing. This sort of lack of robustness is a type of flaw, but not really a bug, per se.

A computer system's function relies on keeping accurate track of what resources are in use. When I program, one thing I have to be careful of in some languages are 'memory leaks'. This is when I tell the computer "hey, give me a chunk of memory to store this picture of a baboon's ass" but forget, when I have processed the baboon butt, to release the memory. C and C++ make it pretty easy to do this. Java and some other languages do 'garbage collection' automatically, but to do so, they have to have considerable resources tied up to act as garbage collectors. There is usually a trade-off between safety of code and performance.

As computing power increases, it becomes more practical to use 'safer' languages, since the performance hit is not so noticeable. It makes it easier for people like me, people who want to use computational power without devoting my entire professional life to it, to still do useful things.

In the olden days (heck, up to a few years ago) it was pretty hard to use things like networking or serial ports without a lot of detailed knowledge of what the hardware and software does when it moves data around. The realization that jobs like this (and stuff like making lists, printing, etc) were being done over and over again made some really smart people start thinking about how to reuse software efficiently. For a long time, there have been 'libraries' of code to help do hardware access, and all sorts of computational and database operations. Still, many of these have been complicated, and most of them islands unto themselves, requiring serious investments of time to learn to use them efficiently. Learning one system might not teach you anything about any other.

Some time back, people started thinking about how they could abstract things, how they could hide details so that a programmer could use a resource without worrying exactly how things worked at the level of individual bits, or hardware.

This has proven to be very successful. Rather than writing data to a location in memory to use a serial port, I can use a serial port 'object' that hides a lot of the crap I don't care about, at least not most of the time. As important, but more subtle, is that this kind of 'object oriented' programming provides a metaphor that can make the whole process seem much more natural. It takes discipline to do well, and I am still a novice. But the force multiplication in this method is palpable very quickly.

Some hardcore programmers resist this. They scoff at people who aren't guru enough to manage their own pointers and memory allocation. They don't want any detail hidden. A real programmer should know how every last bit is twiddled.

They remind me a bit of the guilds of clockmakers who resisted the introduction of standard parts and machine tools. Beautifully crafted timepieces can be made with little more than hammers, saws, and files. But that kind of craft means that every clock has its own personality. When your objective is timekeeping, and not art, then standardization becomes important. I want artisans to keep at it, but I don't want to have to be one to know what time it is. There just isn't time to reinvent everything.

There will never be any system that can't be misunderstood, nor any detail that can't be forgotten or overlooked. And it gets frustrating, ever more so as we all become more dependent on computers for all that we do. The truth is, though, that I really love computers, and the better they get at hiding details, and presenting their resources as abstractions that I can use, the more power they yield. And I dig that.

That's what I'm talking about...

2008-01-22T16:21:00.000-05:00

When I say I've got libertarian leanings, people immediately think I'm a nutbag who wants no government, absolutely no help for anyone, free-market free-for-all, and the devil take the hindmost.

That isn't exactly what I mean. Regardless of whether, in principle, things like police protection and highways could be provided by the market, I still think we have to have government. There are lots of things worth spending money on in our society. It sucks that it has to come out of each of our paychecks, but I'm willing to grant that not every penny of it is wasted by the government.

At the same time, I think that there is a fairly good intellectual case to be made for an observation of Hayek: order does, in fact, emerge out of relatively free markets, and no political hack (or omnibenevolent public servant) could ever take into account the myriad of variables the market does naturally, to solve many problems. The 'invisible hand' may not always tend toward perfection, but it usually gets far closer than any 'best laid' plan ever could. I won't make that point now, if ever. Read Hayek. You may disagree vehemently if you are predisposed towards a centralized, planned economy, but he was prophetic in predicting both the problems and decline of centralized socialism.

Nevertheless, my core reason for even flirting with the label 'libertarian' (which is, in some of my social circles, like 'scientologist' or 'moonie') is my deep belief in the fundamental value of individual rights. I saw something Glenn Reynolds wrote that sums it up for me:

Personally, I'd be delighted to live in a country where happily married gay couples had closets full of assault weapons.

That's exactly what I mean. There are times, no doubt, when the needs of the many have to take precedence, but those times should be few, and far between. People should not harm one another. Past that, leave adults alone, no matter what your personal preferences are. That's what I am talking about.

upside down gidget

2008-01-02T21:36:00.001-05:00

upside down gidget
Originally uploaded by sciencedave

My Coronene buddies posted a cute kitty picture, so I felt obligated to return fire.

This is pretty much how I spent the break, too. It was glorious, but too much free time makes me nuts. I was very glad to return to work today. It is still pretty quiet, with a lot of people not back yet, but I got some chemistry done and some programming figured out, so it was a good day. I missed my afternoon nap, though.

Holiday Hackery

2007-12-21T16:54:00.000-05:00

I received a couple of GPS modules from Ebay over the last couple of days. Along with the ARM board I'm diddling with, I plan to make a device that helps me map my bike rides and walks (both of which are helping me regain proper control of the ankle I had fixed). One of them came with an amplified antenna, so now I have all I need to get my project hacked together. The board pictured is part of an evaluation kit that came with a ridiculously long antenna cable. I'll probably ultimately replace it with a little ceramic patch antenna, but for testing the software and experimenting, this will work fine.

Ebay is a wonderland. I have bought thousands of dollars worth of electronic and scientific gee-gaws for a hundred bucks or so total. It takes a certain amount of determination to find what you want in a form you can use. But I have found super nerdilicious bargains. There is a subculture on Ebay of hackers looking to buy and sell techno goodies, and the best of them will include links to manuals and datasheets. I was able to find all the data on the GPS modules this way, so I knew what I would have to hook up, and how I would need to communicate with the boards long before they arrived.

I plan to spend my free minutes over the Christmas holiday working on making this stuff talk, and gathering data. I saved some vacation time so I could hang out with the family, but after they go to bed, I commence to programming and soldering. And they all like to sleep in, so I have some time in the morning. I should be thoroughly exhausted by the time I have to go back to work. It will be glorious...

Oww, my head...

2007-12-10T23:22:00.001-05:00

Luminary Micros board
Originally uploaded by sciencedave

I have a Mac and several PCs at home. I like my Mac, and usually, it's the only computer that I use at home, because the others are busy looking up ancient ancestors or fighting aliens.

One of my hobbies is programming little single board computers to do nerdariffic things. The one in the photo is especially cool. I won't geek-speak about the details, but I got it for around 50 bucks from a company called Luminary Micros, if anyone is interested. I really like the organic LED display- it is 128x64 pixels, and each pixel can be one of 16 shades of gray. The program running on the board in this picture is just presenting text (and is related to the headache I have), but I have written a Java program that allows me to design graphics for the display.

Macs are not all that popular amongst the engineering crowd, and development boards like this are almost never provided with drivers or software to communicate to a Mac. My goal of using this board (to connect to a GPS, and do some cool stuff) has been stymied for several weeks as I figured out what the hell I needed to do to to make the damned thing talk to the Mac. It talks sweetly to my Dell laptop. But it has nothing for my beloved Apple.

First, I spent a bunch of time trolling message boards and looking for drivers on the manufacturers site. I listened to a bunch of anti-Mac trash talk, but I no longer participate in the techno-religious wars, so I just look for info and go on.

Staring at the board and the schematic revealed that the USB chip is from FTDI, and hot damn, they had drivers for OS X on their website! Which seemed to do exactly nothing. Hmm.

Every chip has a long and boring booklet associated with it called a 'data sheet'. It most assuredly is not a sheet. It is a book. A fairly short, but incredibly dense book full of lots of obscure talk about all the detail necessary to use a chip. They are great when you know what piece of data you are looking for, and indispensable if you plan to actually design something yourself. I just wanted to know why the @#$!% thing wasn't recognized by my Mac.

It turns out that USB is really weird, and every commercial piece of USB equipment has unique ID. This ID is used by the operating system to load the proper driver when you plug in the USB thingy you want to use. The FTDI chip has its own ID, and drivers, but can read external memory and use data there to provide a unique ID for an application.

So, the Luminary board has its own ID. Luckily, I had stumbled on the System Profiler utility on the Mac before, so I recalled seeing lots of data on hardware. When I looked, the info for the luminary board was there. I didn't know what to do with it, but it was there.

After some flailing, I saw a site that had a workaround for using a USB weather station that has an FTDI chip in it. It detailed how to edit a file so that the Mac would recognize the device.

So I tried this, carefully studying examples and copying the data I had found into the right places, and it kinda, sorta worked. But not really. The Mac saw the board, but couldn't talk to it.

So I pored over data that Luminary Micros provided. Finally, I saw it. There are TWO channels in the USB chip. The first is used as a programmer for the chip. The second, ta daa, handles serial communication.

So I changed the file to reflect this arcane bit of knowledge, and it worked. My ears are still ringing from the adrenaline. I choked the mother of 12 bastards to the ground and made it work. Whoo Hooo!

Now, just a couple of months of hair pulling, and I should have this thing done.

Global Fuckin' Warming

2007-11-08T23:18:00.000-05:00

God, how I hate the global warming debate. We can see that some warming has happened, and that we are cranking out carbon dioxide like drunken sailors spending money. The data ranges from the incontrovertible to the asinine, and the projections have uncertainties that dwarf any signal that might be in the noise at the moment, so it is desperately unclear how serious things are or will be, but I actually think that how serious it is won't matter as far as what we actually do goes. I am just going to rant for a minute- I apologize for the lack of links, but I am so tired of all of this that I don't have the stomach for it at the moment.

I am not a denier, I'm a scientist. But I am also one who tries to be a student of human nature a little, and right now, even people who 'believe in' global warming don't believe it enough to do anything different. When the UN flies a shitpot full of people to Bali to have a GW conference, someone is not leading by example, I think.

Is anybody here surprised that the average person, who obviously can't perceive a 0.5 to 1 degree C increase in temperature over a hundred years, who wouldn't know a ppm of carbon dioxide if it bit them on the ass, who has only heard of feedback because of Jimi Hendrix, and who has listened to decades of demonstrably bullshit doom crying and unfulfilled apocalyptic prophesies, doesn't get excited about GW? Really?

Consider: People who absolutely, positively know that they will have to retire some day, who can sit down with a calculator or quicken and project what a modest saving and investment rate would do for their later years, can't be bothered to ever save a dime. And these same people aren't worried about what sort of climate their great-grandchildren might have to contend with? Amazing.

It is not like the scientific community has been all that responsible or reliable a guide when it comes to policy. Much of the trans fats we are so deathly afraid of now came into the food supply because we used to be worried about saturated fats. People have been scared shitless in turn about Alar and DDT and Radon and Saccharine and acid rain and salt. We can do without most of this, sure, and making sure people have some idea of what is going on is, in fact, part of our responsibility; but there has always been a tendency to oversell, and to downplay uncertainties, and the result is that the times we actually need our scientific gravitas to matter, it doesn't. And shame on us for it.

The IPCC projects sea level rises, and so does Al Gore. They disagree by at least an order of magnitude. Both cannot be right, and the best response will, dammit, depend on which is more likely. We could save tens of thousands of lives every year if we would just drive 5 mph everywhere. But we don't. We take some reasonable precautions, and sometimes it isn't enough. We say that life is infinitely valuable, but we really don't think so, based on what we do.

Even if we had a more sober and aware populace, I doubt that democracy is compatible with draconian reductions in emissions that are said by some to be necessary for combating AGW. Kyoto, despite being a convenient thing to hit the US with, was doomed from the start, because no one is going to set their energy usage low enough to hit sub-1990 level emissions. Anyone who tried would be out of office.

So why worry about whether it is caused by humans? (I don't know the science well enough to evaluate it, and am happy to defer to experts, knowing full well that they might be full of dung). So much of the 'debate' centers around this point, and more often than not, GW serves as a proxy for other political commitments. The sticking point is that a vocal fraction of environmentalists see humanity as evil. Right or wrong, it just makes me want to oppose them for being misanthropic and dangerous to humanist values that I hold dear.

(There is some interesting research about how opinions about GW correlate with views on evolution and abortion and all the other issues we tend to line up along. There is no rational reason for this, in my opinion. We just tend to get our opinions wholesale from whichever group with which we identify.)

I'm not afraid to say that, while I think that AGW is happening, and is potentially bad, the current understanding of the science could be wrong, and that we do not know climate the way we know physics and chemistry. There are uncertainties. There are unknown feedbacks. There are errors in the data. There are very reliable observations, too. There are underlying physical processes that are, in fact, well understood, but there are no reliable predictions. There is no existing model that can reproduce the data from the past, so application of a steep discount rate to projections is actually pretty rational, though saying so will often get you lumped in with 9/11 truthers, moon hoaxers, and snake-handlers. Worst of all: There is a dedicated political movement on both sides to demonize the other. It irks me that this has become a quasi-religious commitment.

Instead of penning jeremiads against the eeeevils of capitalism and consumption and fossil fuels, I want to figure out what to do about it, given the fact that we are going to goddamed well continue to extract oil until the rocks squeak, we will burn coal until there isn't any, and we will not consistently elect anybody who tries to stop us once the costs become anything other than abstract. If it turns out that the worst of our fears are true, the most likely outcome, if we go along as we are, is that we will figure out ways to export the misery to someone else. I take the responsibility to avoid this very seriously, even when I can't stomach the extremists on either side.

I despair that people really think that hybrids and ethanol and compact fluorescents will change the climate in a positive direction. It is important to say again that no politician will ever have the ability to do anything like a serious carbon tax, because to do so would be to hand the opposition something very handy to bludgeon the political life out of them.

I was reading one of the UK newspapers- maybe the Guardian- and saw letters to the editor that said, apparently without irony, that man should never have left the trees, that humanity is a virus, and that we must be ready and willing to accept rationing of travel.

Perhaps all three of these things could be supported with arguments, though, frankly, I think all three are psychotically misanthropic, and if not that, at least distasteful enough that they will never be a majority opinion. But unless an Eco-Stalin is in the offing, ain't none of them going to happen, 10 inches or 40 feet of sea level rise be damned.

The unspoken premise is that we are going to be victims, no matter what- either physically or politically, and that somehow we deserve it. This, at the heart of it, is what I object to. I say we can figure out what to do, and can make it happen without destroying prosperity or freedom.

Nature Lovers

2007-10-17T21:45:00.000-04:00

There's not much I can add to this. I like watching nature, too. I'm probably less inclined to hop on it and kill it than my cats. Probably.

Scientific Methods for Kids

2007-10-04T12:12:00.000-04:00

I was looking through ancient emails, and found one from my niece about a school project, which was supposed to be about a controversial topic. She chose researching whether HIV might be a bio-engineered weapon. So she wrote the family scientist Uncle Dave about lots of troubling stuff she had read. I recall talking back and forth about her project a few times, but in the beginning, I wanted to equip her with some basic skeptical attitudes. I'm not sure of all my facts or reasoning here, as I wrote off the cuff. My goal was to seed the conversation with humor and skepticism from the beginning, so I responded as follows:

Grandpa said you were going to email me about HIV or something. I’d be happy to help you evaluate whatever evidence you want to look at. I’ve heard those rumors about AIDS coming from a bioweapon since I was at Thomas More College (around 1988, I guess), so the idea has floated around for a while. I have not followed up at all until today, so I don’t know the state of the argument. I will say it does not get play in peer-reviewed science journals, which are not the ultimate arbiter of truth by any means, but they let you know what experts are up to, and what they think is important.

I am a little skeptical, though, for a few reasons involving the most basic science, psychology, and politics:

1. There is no story except at the very fringe. All big revelations start like that, you might think, but they only start on the fringe, and quickly become pervasive. The value of breaking this story in a credible fashion is hard to calculate, but it would guarantee some journalist’s career, even their place in history. There are a lot of fearless people who would not be dissuaded by less than credible fear of death, and some that would not be dissuaded even at that, who would love to expose this if it were true.

Politicians would salivate even more than journalists. Imagine if Republicans could prove that HIV was developed when Carter was president. Boy, Howdy! Or if someone had documents showing Ronald Reagan had commissioned research to develop a means for controlling the weather as a weapon. Science aside, the payoff politically would be huge, and there would be more people killed in the stampede to use the information against the other side than die from dread disease in a year.

This is not disproof that HIV is a bioweapon, and I don't want you to think that I am ridiculing the idea, but it does calibrate just how clandestine, and therefore expensive, it would be to keep this secret from the thousands of people all working independently on HIV. To be this expensive, it would have needed to be a very important project indeed, and for reasons I’ll give later, I think it could be argued logically that HIV is a emphatically not a valuable weapon.

2. Some people argue that ‘they’ (they could be the govt, the media, evil scientists) are keeping it a secret. Not likely, for the same reasons as in number 1. There have certainly been things that have remained undercover- the Tuskegee Syphilis experiment went on for a long time, and was racist and evil to the core. However, this was in a time when the money, fame and available outlets for exposure did not exist, and it was done to a group that was ignorant of what to expect in treatment and powerless. Notice that once outlets did exist, the story came out! Things that could be concealed 50 years ago would be damned near impossible today, and victims of AIDS, though tragic, are rarely ignorant or powerless, at least in the US. Keeping secrets gets harder and harder, especially those that require lots of people who are not easily controlled.

A favorite 'they' is evil scientists. I'd be the last to suggest that there are not evil scientists. But 'scientists' are not members of some sort of well-coordinated organization, and getting scientists to either cooperate or be quiet is not a task that I think anyone could do for long. Scientists worked in secret on the atomic bomb, but only a few, very isolated, for a few years. It is hard to keep technical secrets.

3. If HIV is a bioweapon, it certainly isn’t a very good one. It really isn’t transmitted very easily. It has a very long incubation period. Weapons are supposed to do something to someone. Generally, you shoot someone because you want them to stop doing something (beating you up, shooting you, stealing your money, occupying your land) in a relatively short time frame. You wouldn’t stop a robber by giving him AIDS. Serious bioweapons like smallpox or anthrax are much more deliberate and quick killers. If anyone wanted to rid the world of gay people, AIDS wouldn’t do it, because it is easy enough to avoid. Governments that spend gazillions on weapons expect them to work, and quickly. Maybe a failed bioweapon? Maybe. Is that really more likely than a natural source, though? And to what end? What is it that could be gained by doing this? Evil is an expensive business, and 'they' want a return on their investment, I would guess.

4. There is a lot of independent scientific work that shows that HIV is very closely related to an SIV (simian immune virus), and that it is a simple and not human-caused set of mutations that caused it to jump species, probably in Africans that butcher and eat apes. This is a known route for trans-species infection (just like the bird or swine flu varieties that break out in human populations). There would likely be markers if HIV had been human engineered, because genetic engineering is done by very specific methods, and they leave tracks. And people are not smart enough to ‘create’ a virus yet. They can recreate one that already exists, but that's a different task.

5. HIV sucks, and people think of it is as horribly dangerous, but compared to what? No one believable claims that Spanish (or bird, or hong kong) flu is a bioweapon, and they kill or could kill a lot more efficiently. 20 million in 1917-1918 by flu vs 32 million worldwide from HIV from the 1980s till now. I think that because certain populations that are most likely to transmit HIV are also sort of persecuted in other ways, they might feel like it must be a plot against them. If everybody got it easily, it wouldn't be a 'gay' disease (which it isn't, but for the practices of gay men that put them at special risk) and the fear of it causing, or being because of, homophobia would be less pronounced.

6. Transmission by IV blood exchange or by fairly (ahem) vigorous sexual contact is unlikely a weapon designer’s goal. Nor would it be likely that one could single out these factors.

7. What little looking I have done shows classic, paranoid and unfounded innuendo rather than scientific arguments to support the claim. The basis of the argument often seems to be “Since they (government, racists, corporations, jihadis,whoever) has done evil in the past, and they would like to get rid of (blacks, gays, foreigners, infidels, communists, whoever) then it makes my theory plausible”. Well, not really. Yes, all those guys are capable of evil, and yes, many have groups they’d be happy doing evil to. These facts are independent of whether there is evidence that someone in fact did create HIV as a weapon. A Klansman might cheer for sickle cell anemia, but that doesn’t lend credence to the idea that the Klan bioengineered the malady. Wicked for cheering SCA, yes. Responsible for developing SCA, well, no.

8. A favorite tactic of people pushing extreme ideas is “Well, how do you explain X?”, with a lot of knowing innuendo and looks, as if a question proves anything. The answer is first I’d have to believe that the burden is on me to prove or disprove the bioweapon theory, which it isn’t. This doesn't get said often enough: the person making a goofy-assed claim has the responsibility to prove it. The logical extension of this is something worth internalizing: When someone makes an assertion that something alarming is true without providing evidence for the claim, you are free to not respond to them at all. You do not have to refute a claim to be free of obligation to believe it. This is not well understood. You carry no burden to believe or refute something someone says. If they present no evidence, there is no burden on you at all. It all rests on the person claiming that an invisible dog talks to them, or that HIV was developed by the CIA, or that the Roswell aliens gave us the technology to make Pringles. They may call names and says things that they think are very meaningful like "You need to wake up!" or "Don't be a sheep."

But playing along, I’d first have to be certain that X needed explaining. It might be wrong, made up, or obviously explainable. If it was none of these, I’d evaluate the evidence and look for what it means. At the end though, remember- the guy with the theory is obliged to prove it, and we have no burden one way or the other. No proof, and you are justified (scientifically, even) to just shrug and go about your business.

Don’t be dissuaded, though. None of my arguments are disprovers, just reasons to require very high levels of proof. Find out what you can. We can run it through the bullshit detector and see if anything survives. Real evidence would likely be pretty technical, but that’s what I’m for. Let’s see what turns up, if you want.

incisions, incisions...

2007-09-28T00:21:00.001-04:00

incision
Originally uploaded by sciencedave

Some people who have known me for a long time know that I am something less than graceful. Lumbering, gorilla-like at times, or more like a cross between lizard and weasel when I get hyper and excited. But absolutely, positively not a natural athlete. Coupled with bad eyes and poor coordination, you'd probably expect that I spent my youth squirreled away in books, or taking apart electronics, and avoiding sports and adventure.

Well, I was bookish, and I tore apart everything I could, and reassembled some of it into things far more dangerous than what I began with. But I was a pretty vigorous kid. I climbed trees and dug holes and waded through creeks. I pursued and caught all manner of insects and animals, some that punished me severely for my efforts. I played sports, even some that I sucked at so badly that all I ever got was knocked down, because it made me feel good to contribute even if only by being ballast. And I learned to put body english on other players, so my just-above-average frame saw lots of contact, and more than a few fist fights.

I was a nerd that had a big mouth, and who wanted to get along with the cool kids and the jocks and the stoners as well as the nerds. I wanted to be friends, but I had a lot of pissy Irish pride that I got from my Grandmother, and I was willing to fight any and all of them for respect.

I climbed rocks and rappelled down them in college. I ran, and played some silly intercollegiate sports. The great turning point came, though, when I had a brief dalliance with the military about 21 years ago, where I again ran afoul of every rule and obstacle in my way, and yet learned valuable things that have never left me.

I came in and they warned me that I was not allowed to join due to my status as a seminary student, as it turned out. That they would consider discharging me right away. I didn't want them to, despite also thinking that I had arrived in the Inferno. So I talked them into seeing if my status as a 'divinity student' could be changed, and embarked on the torture gauntlet that is basic training.

In the process of learning to shoot and bayonet and march in formation and deciding that I would tell the seminary to (ahem) go to hell, I twisted my ankle so that it swelled up as big as my thigh. Uncle Sam gave me some cortisone shots, a check for my troubles, and a bus ticket home. I have nothing but respect for warriors, and did what I could to join them, but I think, frankly, we were better off without one another. I don't regret the attempt, and I am glad for the resources they uncovered in me.

It took a while to recover, and I never really thought, at 22 years old, and despite my injuries, in the best health of my life, to go have a doctor look at my sore foot. So it sort of healed. And I re-injured it, again and again over the last two decades.

This last time, a few months back, it wouldn't get better. Xrays and MRIs later, they explained what I had been doing to my unfortunate body since the mid 80s. The posterior tibialis tendon was frayed and slackened by repeated tears. My arch collapsed. The insults sort of radiated up my leg, and caused some degeneration in my knee and hip.

So, the nice podiatrist referred me to a surgeon, and she repaired the tendon, and put a titanium pin about the size of a thimble in my tarsal sinus . And I am crutching, in a cast, for the next 6 weeks, having spent about 2 weeks already.

For a while, I was in a vicodin and vistoril haze, but now I have no real pain, just boredom and immobility. I just started going back to work, and have been keeping busy with data analysis and programming. But if everything goes right, I should get back, approximately, the foot I haven't seen in 20-odd years. If I can believe my doctors, I will be able to run and bike without worrying about my stupid foot. I'll still be clumsy as an orangutan, but that's OK with me.

Anniversary

2007-09-26T17:28:00.001-04:00

our 1st married dance
Originally uploaded by sciencedave

Today is my 15th wedding anniversary.

My wife and I met in the most random, unexpected way, at a traffic light. I was friends with her brother, and we had been out to eat. I saw the cute pizza deliver girl gesturing to get his attention. I said, "Hey, this chick's trying to get your attention." He said "That 'chick' is my sister."

A couple of days later, my buddy called and said, "You ought to ask my sister out on a date". So I did.

At first glance, we were not much alike. Neither of us had any idea that by the end of the first date, the die was already cast. We talked and laughed like friends long before we became anything else.

I am a lucky, lucky man. My wife and I don't see eye-to-eye on some things, and we fight like weasels on occasion. But we share a sense of humor, and she is good, honest, and incredibly supportive. She pulled things from inside me that I never knew existed.

If it were not for her, I would not have the children that have shown me the purpose of life. I would not have pursued the career that sustains my mind and provides our living. I would not have faced truths that had consistently come between me and success. In some ways, I would simply never have become myself.

Most of all, though, as I rediscover again and again, she is my best friend, my most loyal ally, my team-mate, and my partner.

Periodic

2007-09-08T22:59:00.000-04:00

I left the following as a comment on another blog:

I have a buddy who is a communications professor. He speaks the Gramsci/Foucalt lit crit hegemony stuff all the time. Mostly, I haven't got the first goddammed idea what he's talking about, though I have given it enough of a try to encounter the Sokhal hoax and stuff like that. But once, he asked me what it would take to 'overthrow' the periodic table. I tried to make the point that, fundamentally, the periodic table is an organization of experimental observation, that has since been backed up with theory. He wondered why we 'privilege' this particular structure.

After trying really hard to understand what the hell he meant, I got the impression that he thinks, honestly, that scientists just make shit up and all agree to discuss it in a certain way. I basically told him that he had the luxury of this because he didn't interact with things that would mercilessly render him dead as a rock if didn't privilege the knowledge that has been gained over time, different ways of knowing be damned.

He thought, and then said, "Yeah, if I write down something that doesn't conform to the narrative of my field, my papers won't explode." I think that we may have understood one another for a few minutes, at least.

I used to think that it was just a caricature of loony professors that allegedly actually believed that science has no basis outside the conversations that scientists engage in. Admittedly, this is the strongest of a continuum of such positions, but I am beginning to realize that some people really think that this is true. I can't relate, but it is intriguing. I suspect that this is actually a posture that some affect, and that with experimentation, one could uncover a basic belief in physical reality that would belie this academic position.

update:Thanks to Ms. PsiStarPsi for catching a broken link. It looks right in HTML, but apparently, blockquotes baffle Blogger. Or maybe it's just me. The Sokal Hoax I refer to above was the demonstration by Alan Sokal, a physicist, that much of the 'scholarship' in the literary criticism and social sciences fields is little more than posturing, especially when they try to apply scientific concepts. The affair is still stinging to some, and some legitimate questions have been raised about exactly what Sokal proved. It just shows, in my mind, that if one follows the dominant narrative in social sciences, they don't care whether what you proffer as arguments are correct, or even meaningful.

In fairness, I do acknowledge that plenty of science is, in fact, socially constructed, and scientist are pretty naive about this. It is the prevailing consensus that drives what people choose to research, which de facto decides what gets funded. There are also plenty of gender and race issues in science that others are far more eloquent in describing. So I don't mean to suggest that social science is all bunk. In fact, I think physical scientists would do well to learn a bit about it, especially economics and sociology.

What I really object to is that the strongest holders of the position that all knowledge is socially constructed ignore the fact that we do, in fact, spend most of our time being wrong in science. If it were possible for a cabal of scientist to decide, by consensus, what counts as scientific fact, falsifiability would not be the center of our discipline. This lack of responsibility to something external to the community, and the lack of falsifiability, are really the points where other academic fields diverge from science. So far as I can tell. Maybe I'm deluded by the patriarchal, capitalist hegemony into believing that I shouldn't mix elemental Fluorine with Cesium metal, and perhaps a Wiccan High Priestess could do so because she isn't bound by my reductionist blinders. I'm still going to leave the room, just in case. And, in the end, science wins, because even this would be empirical knowledge. Next, we figure out which solvents dissolve Wiccan Priestesses...

dandy

2007-09-05T10:47:00.001-04:00

dandy
Originally uploaded by sciencedave

These two seed heads were spotted by Sam, my elder son, on a walk. He wanted to know if these were evidence of evolution. I admitted that I couldn't be certain, but that it seems likely to me. We talked a long time about how life must have gotten started, which is something that I have found interesting since I was a kid.

Once one understands the implications of evolution and abiogenesis, there is the problem of how life got started. I recall how fascinated I was when my dad told me about the Miller-Urey experiment, and I have continued to follow this a little. A.G. Cairns-Smith, who has suggested that early life, before DNA and RNA, might have been templated by clays is especially compelling to me, though it hasn't been widely accepted. It is, though, an attempt to wrestle with this difficult question of how life could get started. If it is totally wrong, it is still important because it tries to see the steps involved.

Professor Cairns-Smith was kind enough to send me some signed galleys of a chapter he wrote for a book on the origins of life that covered this back when I was a post-doc. I used them to prepare a lecture on the origin of life that my physicist advisor included as part of an intro astronomy class. It was great fun to tie the explosion of stars to clay to life to Steve Buscemi in 55 minutes...

Despite some of my organic friends alleged hatred for "icky metals", a lot of organic chemistry's contribution to biology is in holding an icky metal in just the right place to do something important. The interplay between all of science, especially when it comes to understanding what we are and why, is something that I am still trying to comprehend.

Time Machine

2007-07-21T00:32:00.000-04:00

I first programmed a computer in 1977, when my best bud got a TRS-80. We had an enormous amount of fun doing this, and I owe a lot of what I do now to those days. We used the thing pretty much every day until around 1980, when he spilled a glass of orange juice on the keyboard, which is where the CPU and everything else lived.

A really neat simulator of the TRS-80 is available on the web, running as a Java Applet. So, essentially, a web page today can be what a computer was 30 years ago. You can enter and run programs in the window, which looks just like the screen of the TRS-80. I immediately wrote and ran a couple of programs I recall writing back then. It was weird, like seeing my own life simulated on a computer. Or like stepping out of a time machine. As non-descript as the TRS-80 was, it occupied a lot of mental and emotional real estate when I was 13.

One kind of funny point- the simulation runs considerably faster than the original computer did.

Science has it all...

2007-07-12T21:52:00.000-04:00

One of my enduring interests outside science is economics. I don't get jazzed about the stock market or exchange rates or GDP, though, which is what I used to think economics was all about until I took a fabulous Microeconomics course from Mel Borland at Western Kentucky University. I took it because I needed credits to graduate, and suspected that I would hate it less than alternatives. I loved the course, and I left the class a different human being than when I entered it.

Economics, as a social science, is about allocating resources, resources that are limited, in order to get the most out of them. The goal is to provide the most happiness, or utility, or whatever variable you decide to maximize, at the lowest cost in effort, dollars, etc. Economists in the US tend to measure things in dollars, but one can pick whatever one wishes as a basis. Dollars are just an abstraction, to quantify something that we tend to believe, with little justification, to be ineffable.

If you have ever heard of the philosophical construct 'universal acid', an acid that dissolves everything, you get a sense of how I felt when I first began to grok economics. While there is always some irrationality in human beings, analyzing actions of people (especially in groups) as rational actors, seeking to maximize gain for a given investment, is a tool so powerful that is is easy to become quite intoxicated by it. It transcends very quickly the problems about supplying widgets at a given price. It helps to understand human behavior. Buying stocks, choosing a mate, making life or death decisions, all involve this sort of calculus, and while social mores tend to obscure them, recognition of them is, to not put too fine a point on it, majestic.

It is really easy to fool yourself into thinking that you and everyone else just automatically understands this stuff. But when you find yourself thinking "There ought to be a law limiting what they charge for gasoline" you generally ignore the fact that price controls inevitably lead to shortages. Inevitably. Gasoline, apartments in New York, whatever. And price floors lead to surpluses. Inevitably. People will argue with you until they are blue in the face that the minimum wage will NOT cause unemployment, but that is generally because anyone conscious of the issues is already making much more than that, and has no direct experience.

Statistical shenannigans and outliers will be trotted out about minimum wage, because it has such a personal face, but if you substitute anything else- say, TV sets- and say "No one can sell a TV set for less than $250", would you be surprised that fewer were sold than when the price could, in fact, go lower? How much is it worth to greet people at the door at X-Mart? As soon as it isn't worth it, would you expect someone to pay for it?

There are also dangers in over-simplification, and I don't mean to pretend that Econ 101 explains everything, or that the world is not in need of lots of serious reform. But Physics 101 doesn't, either, but someone with that level of knowledge is still miles ahead of someone who lacks it. Economics is like physics- fairness and gravity are unrelated, as are fairness and what people actually do. Not what they say they do, mind you, but what they in fact do. The most sublime bridge or skyscraper must ultimately bow to the laws set out in basic physics, or tumble to the ground. Similarly, basic econ knowledge can act as a preliminary 'bullshit detector' when considering what some cobra/politician is suggesting.

Econ gets obscured in the news, largely because reportage is unburdened by even the mildest familiarity with basic econ. But there are a handful of great books available to the interest layperson. Some of my favorites are David Friedman's Hidden Order: The Economics of Everyday Life, The Undercover Economist by Tim Harford, and Freakonomics by Levitt and Dubner, though Freakonomics is probably as much sociology as econ. Harford's book is especially recommended, especially if you have ever wondered why Africa stays poor no matter how much money we pour into it. (I apologize for the lack of links. Blogger pukes when I try to insert an Amazon link, and I am not in the mood to figure out how to do it by hand.)

Not only is economics pretty much understood, it can be pretty unloved, too. Bjorn Lomberg is a statistician/economist who is completely in agreement with Global Warming theory. He is convinced the world is warming, and he is convinced humankind is responsible. But his book, The Skeptical Environmentalist, committed the faux pas of considering how our (limited) resources could be spent in mitigating all of humanity's problems, not just AGW. And his contention is that Kyoto (for instance) would do almost nothing, but would consume so much money that things like disease control, hunger, poverty, the lack of clean drinking water, etc. would need to be forgotten. At the same time, he calculates (and not just him- see the Copenhagen Consensus for more details. Denmark is not exactly a neocon hotbed) that we could pay to solve all these other problems and adapt to global warming with the same money that would have no real chance to stop global warming. Bjorn excites a lot of passion, which is unfortunate, because people see environmental issues as proxies for left/right political issues, and ignore the data.

This sort of thing brings me back to reality. Physical science, at least at the hard edges of physics and chemistry, generally will yield a definitive answer, given time, money, luck, and careful experiments. Econ, not so much. I am reminded of the words of the great sage, Principal Skinner from the Simpsons:

Ah, there's nothing more exciting than science. You get all
the fun of sitting still, being quiet, writing down numbers,
paying attention... Science has it all.

Science-riffic

2007-07-11T02:46:00.000-04:00

In his July 1, 2007, New York Times Op-Ed piece, "Moving Beyond Kyoto," Al Gore states:

Consider this tale of two planets. Earth and Venus are almost exactly the same size, and have almost exactly the same amount of carbon. The difference is that most of the carbon on Earth is in the ground - having been deposited there by various forms of life over the last 600 million years - and most of the carbon on Venus is in the atmosphere.

As a result, while the average temperature on Earth is a pleasant 59 degrees, the average temperature on Venus is 867 degrees. True, Venus is closer to the Sun than we are, but the fault is not in our star; Venus is three times hotter on average than Mercury, which is right next to the Sun. It's the carbon dioxide.

OK, look: I think Al Gore might have gotten the shaft in the 2000 election. I will give him the benefit of the doubt on the political end of Global Warming. I think he wants to do right by the planet. He is a smart guy.

But to compare Earth and Venus- Earth with less than 0.04% of its atmosphere carbon dioxide, and Venus, with an atmosphere that is 96% carbon dioxide- and to think that this comparison is relevant must be the product of abject contempt for his audience, or downright stupidity on his part.

The fishy part isn't the plain statement of fact, about the distribution of carbon. By comparing the two, though, he implies that Venus is somehow a model of how Earth could be. First, it isn't just carbon dioxide- Venus' atmospheric pressure is 90 times that of Earth, and this huge density difference matters a lot. With the projected doubling of CO₂ that might happen by 2100, we'd still have less than a tenth of a percent CO₂.

Gore's statement that the relative position of Earth and Venus isn't important is also suspect. It is thought that the boiling off of early Venusian seas might be responsible for the accumulation of CO₂ in the atmosphere.

As nitpicking as it might seem to bitch about these points, there is something well worth bitching about: if you want to make scientific arguments, make sense. Don't overstate any effect, oversell any model, or overstate certainty. Don't hesitate-no, rather rush headfirst- to admit deficiencies, error bars, and confusion.

My darkest fear is that he knows that this is crap, but thinks that it sounds like it would be effective. As a scientist, I am offended by that thought, though I don't accuse him of it. I just fear it.

The really irksome thing to me is that I hear people beginning to conflate Al Gore with the science itself. To criticize Gore is to commit a moral wrong, equivalent to not believing 2+2=4. Well, bull-fucking-shit. One can argue that Gore is right and virtuous to lead the fight against Global Warming, to which I say, OK. But if he gets scientific things wrong, then I owe him nothing but criticism of the science.

Shrinking from direct engagement of skeptics is troubling, I think, since the data and models ought to be such that anyone properly trained can examine the data and models, and deduce the same things. But the protestation that the science must be accepted is just the thin film over something else entirely. The subtext is that the regular folks will be lulled into thinking that there is nothing to worry about, if the uncertainty is revealed. So the disbelievers have to be silenced.

The Tobacco companies are always trotted out as examples of evil, misplaced skepticism, as sowers of uncertainty and discord, as deniers. The problem with this analogy is that Big Tobacco was not beaten down by ignoring the uncertainties in the scientific study of tobacco's health effects. To the contrary, the battle was won by continuing until the evidence was overwhelming.

The much bigger worry is that people will be cowed into believing something that requires a radical response on thin evidence, and will concomitantly be brow-beaten into acting before proper cost-benefit analysis can be performed.

This last point may be lost on politicians (and non-scientists in general). Things like relativity, or evolution, or plate tectonics, do not spring fully formed, with all the details worked out, from the scientific community. Things have to be figured out. If you follow climate science, which I do only as a spectator, you can see that despite the general picture of GW being figured out, the details are very much in flux.

It is damned rare that even good understanding of problems leads, smoothly, into public policy. I, for one, am delighted that there isn't a yearly malaria epidemic in the US. That DDT was used willy-nilly to get to this point inspires less delight. The trade offs necessary to achieve huge goals are often ugly, akin to warfare. This isn't the sort of thing that I want to be driven by half-assed science.

Appeals to scientific consensus are even more misleading, and horrific, than even goofy or misleading scientific analogies.

Consensus, indeed! For scientific revolutions to occur, after all, the consensus must be, at some point, dead wrong. It takes a while to get fairly accessible, well defined problems figured out. Climate is neither accessible nor well-defined, and the best models going ignore things like clouds and aerosols. So when Gore or the like says "the science is settled", I don't hear bright peals of scientific enlightenment. I hear the crackle of kindling, ready to burn the heretics.

Oh, and Live Earth sucked. Or so I read, because neither I nor anyone I know (a group that includes more than one rather fearsome greenie) saw any of it. I don't owe anyone any fealty for good intentions culturally any more than I do scientifically. Watching Madonna was something I last did in the early nineties, and not on purpose then.

Gorgeous Tiny Chicken Machine Show

2007-07-07T23:29:00.000-04:00

Has anybody else seen this?

I like it, but I am uncomfortable with it all the same. Not 'uncomfortable' meaning 'back off me with that shit', which is how I would describe how people use scare-quote "uncomfortable" in my native tongue. Or they say that they're "not OK with that", a construction so pinched and constipated I tend to forget that people actually say it. I think I might even say it by accident, occasionally, when someone else in my group says it. Apparently, the pack instinct overrules the more lately evolved sense of grammatical propriety. Hypocrisy, perhaps, comes naturally to us when we try to get along with one another. It's a social lubricant. As is overlooking it.

No, I mean it makes my skin crawl- not the show, but my inability to identify what I find compelling in it. Perhaps it is the multi-reflective nature of the comedy. Are we making fun of Japanese people (I don't think so) or are we poking fun at their picking up tidbits of American culture and making them something and misunderstanding them? That doesn't seem right, either, but as the complexity or subtlety of the explanation increases, I'm going to be less certain.

I'm a Nipponophile. No, I don't mean I dig Japanese women. At least not exclusively. I mean that I find a lot of Japanese culture compelling. Samurai and ninjas alone would have made them one of my favorites. Zen. Stuff westerners like to appropriate and use inappropriately (at least from the point of view of the originators of the culture). I know I do. Samurai rock. As do ninja. And Zen monks. A zen monk samurai ninja...

I've seen Japanese television a few times, so part of my impressions of Japanese culture is based, inevitably, on my unfamiliarity with how they roll in Japan. Just after my wife had our first kid, we lived in an apartment that came with satellite TV service. It just so happened. We never knew until we moved in.

Each day, for some short time (which I never bothered to measure- on the order of 1 hour) we got Japanese news followed by a japanese entertainment program. They were always incomprensible to me; sometime staid, sometimes frenetic. Despite my lack of understanding, I found it riveting. I didn't understand why. This is sort of a pattern.

I often encounter things that I find impenetrable. Certain parts of physics and mathematics have proven to be like that. Lots of art and music as well. In art and music, I can find accessible background to help me understand what people are up to. The same is true of science and math, too.

Java for Chemists (and other ne'er-do-wells)

2007-07-01T21:10:00.000-04:00

I am starting a series to introduce Java programming on another blog. I hope that I can interest science students in this- Java has become a very powerful tool for scientists because it can be used at a high enough level of abstraction that many of the low-level details usually involved in programming can be ignored. There is a performance penalty for this, but for most people not in the business of writing software for a living, this trade off is well worth it.

I am not an expert at Java. I have been programming in C and C++ for almost 20 years, though, and I know how unrewarding these can be for someone who is interested in just sitting down and getting the computer to do something, and who doesn't want to get lost in a dense thicket of details. Projects that were at the outer edge of my abilities in C++ were doable with a couple of months of experience with Java programming. It is tempting to think that this is because I had a lot of experience with C and C++. I think that this may have helped a tiny bit. But a lot of the magic of Java is that it takes care of many things that cause major hair-pulling in these other languages. If you don't know what I'm talking about, be glad. The kind of crap that one has to deal with in C and C++ is one of the reasons that most people don't think of them as part of their toolbox. Java offers most of the power and performance of these, with far, far less hassle. It says something about Java that I am willing to present it to others with less than a year's worth of experience. I won't make anyone a computer scientist, but I can help scientists get some really cool things done with their computer.

My aim is not to convert anyone to the First Church of Java. I aim to present Java as a tool for scientists and technical people, and I hope to do so with interesting and fun examples, with games as well as with simulations rich enough to offer a little insight into physical processes. I will not be exhaustive- there are many fine tutorials available, free of charge on the web, that do the job far better than I can, and I will refer to these with abandon. My job will be to hand-hold a little, point to information of value, and to show what can be done with a surprisingly small amount of effort.

Prefab

2007-06-22T00:26:00.001-04:00

Breakfast
Originally uploaded by sciencedave

There are a lot of things that I ate as a kid that I wouldn't dream of consuming today. Lucky Charms cereal leaps to mind. Vienna sausage. Ho Ho's. Choc Cola. Yoo Hoo. "Chocolate" covered donuts.

I can't quite find time to be the epicurian that I would like to be. Leaving aside preparing gourmet dishes, I find it difficult to find time to prepare even simple homemade fare, which makes me sad in a way that I find surprising and unexpected.

I'm not talking about being some sort of strident food fanatic. To find myself thinking seriously about my 'relationship' to food is a bit touchy-feely for me. I tend to be suspicious of that kind of facile emotionalism, especially when it comes to something so central to life. While I am not begrudging anyone their own choices, I don't have the patience to be vegetarian, even if I were so inclined, which I am not. Veganism is a slightly different matter, in that seems determined to convert others- it strikes me the same way snake-handling pentecostalism does, as something that probably started harmless, if goofy, that ended up going horribly awry. I dotake exception to especially self-righteous food-nazi's trying to make decisions for everyone else.

I recognize that food is a huge business, and there's plenty of yin and yang involved in it. Yes, it is a corporate behemoth that is driven by nothing but profit. But without it, and mechanized and chemically supported agriculture, most experts believed that we were headed for massive starvation by the early 1980s(some of these same prophets of doom wished openly for this- any considerations about environment notwithstanding, these are self-worshipping, racist moral cripples). I shudder when I hear anyone use the word 'sustainable' in front of agriculture, because most of the plans I have seen sacrifice the lives of brown people in far away countries on the altar of an eco-utopianism practiced by vapid SUV-driving soccer moms. Sure, there is plenty to decry in mechanized, industrial agriculture, but it is still fucking creepy to wish for the deaths of a large fraction of humankind.

Yet there is something sort of soul-killing about all the prefab crap that makes up the diet of so many of us. Stuff we know isn't good, but that we can't quite figure out how to escape. Stuff that mocks the idea that we ought to be eating good stuff with people we like. Preferably at less than 90 miles an hour.

I am a pretty good cook. When I can find time, I can put together a tasty meal from fresh ingredients that leaves us wondering why we ever do anything else. Which we promptly forget until sometime a month or so down the road when one of us has the time to do the same thing again.

I'm not going to preach against Pop Tarts or Mountain Dew. Despite my anxiety expressed above, I think that this sort of food is inevitable, given our values, and not altogether bad. But given the path of least resistance provided to us in the form of processed, prepared and packaged gustatory delights, we have to make a conscious effort to include things that are more appropriate.

I started my children eating fruit and vegetables at a very young age. Both are avid munchers of apples and raisins and so on, and are not completely seduced by junk. But they'll eat garbage with just as much enthusiasm as bananas, so I have to make the effort to keep the good stuff available.

The drive to pack as much into the day as possible is taking a toll, and disrupting an important part of life. I'm not precisely sure how to alter things, but it's my nature to experiment.

toxic finger

2007-06-20T16:33:00.001-04:00

toxic finger
Originally uploaded by sciencedave

I didn't realize I could post my Flickr photos directly to my Blogger account, but now that I do, I will.

Globally Warmed Over

2007-05-31T13:18:00.000-04:00

I am not a global warming denialist. I need to state this up front because I usually get mistaken for one when I point out that no political mechanism exists to mitigate AGWs effects. I also think that there are enough uncertainties in the degree and effects of warming, and enough uncertainty about what might actually help, that I am dubious about most prescriptions for actions.

Specifically, the imposition of any measure that is going to cause serious economic pain (which I suspect will be necessary if one is to stave off AGW's effects) gives an automatic opening to a rival party to make hay by offering to repeal it.

It should be clear that we are talking about taking actions now that will not yield all of their fruit for generations. Even if we could get people to acknowledge the usefulness of (for instance) a high gasoline tax, how would it 'stick'?

Climate is big, it has a lot of hysteresis, and will do confounding things, like unexpectedly going counter to the underlying trends for years. If you think evolution is a hard sell, just wait til AGW mitigation actually means that someone might not get to drive their SUV to the "Inconvenient Truth" screening.

We generally won't save money for retirement, as a culture, and we know that old age looms for all of us. We sometimes say we want to protect the children, but there is usually a fight about any taxation for schools. Who wants to pay 5 bucks a gallon for gasoline to keep our great great grandchildren comfortable? (I am being frivolous on purpose. I understand the gravity of the problem. I just don't see what to do about it.)

Note that this is not an argument for doing nothing. It is a cold, scary suspicion that this kind of problem may be outside the purview of politics as it is practiced. The world might hand the keys to a science-based policy that would cause deprivation and economic pain for a couple of years if something obvious and immanent were coming, like an asteroid.

My other dark suspicion is that AGW is, for most people (acknowledging that most people lack the skillz to calculate their own BMI, let alone evaluate climate models) a proxy left/right fight, where, since the US is doing approximately nothing about it, one can choose sides at nearly zero cost, lazily picking whatever their political affiliations suggest. Put less unkindly, few actually evaluate evidence because there is currently no penalty involved just going along with their 'side'. And people haven't gotten completely sick of the climate pr0n on the weather channel, yet.

My prediction- climate change denialism will become more fashionable the more is done to confront climate change. People are great rationalizers. When the money comes from their pocket, the data will suddenly be less clear. I suspect that the underlying science has the most acceptance and support it will ever get at this point now, before anything gets done. Once someone pays, sides will shift.

Yes, as a matter of fact, I am bitter, cynical, and slightly misanthropic.

Who's programming who?

2007-05-29T22:30:00.000-04:00

I write a lot of software to collect and process data. The reasons and data itself is pretty much top secret, but some of the details about how I do it might be interesting, especially to the science types that wander by.

I am not a general-purpose programmer by any means, and I would hang myself if I were responsible for anything called "business logic" or database analysis or the kinds of things my 'real' programmer friends do for a living. I have one buddy who has done some interesting programming for the military and for phone network switching, which sounds kind of fun.

Some stuff I do falls into the area of embedded programming. Imagine your VCR, or your car, or your favorite piece of laboratory instrumentation. It's common knowledge that these contain microprocessors or microcontrollers, and often more than one per device. Embedded programming is the programming done to make this hardware work. Usually, I do this in C these days, but years ago, I did it in assembly language (thinking about this too much gives me the shakes...). There are usually no graphics involved, except maybe an lcd screen, though this has begun to change. Everything is done from memory, there is no operating system (again, this has begun to change as Linux is ported to microcontrollers). In most cases, I have done this to automate some data collection in an instrument that had to be custom built for some reason. Generally, if I can figure out how to do a project with commercial instruments, I'll do it that way, because the time involved in writing any software, but especially embedded software, is amazingly long.

At the extreme opposite of this is programming in LabVIEW. LabVIEW is a graphical programming language designed to allow one to string together instruments, controlling them and gathering data from them by essentially creating diagrams of their interconnections. It is much faster, in most cases, than procedural programming, but it isn't hard to do it really poorly. There really isn't any tool to protect you from the need to think clearly and logically. LabVIEW contains all sorts of mathematical and graphics functions, too, so it's not too difficult, supposing you really think through the logical tasks, to make spiffy, extremely useful software.

I have a handful of tasks where I have used LabVIEW to control a box that contains a microcontroller that I programmed in C to do some task. This combo is really powerful, because you get the fine-grained control of exactly what your hardware does using the embedded computer, but then the data you gather can be displayed and reported in a beautiful, professional fashion.

My latest foray into programming is Java. For years, I have been avoiding it. It always seemed slow and incredibly obtuse. But over the years, apparently, it has begun to get better and better, and best of all, there are lots of really fantastic tutorial and reference materials available on the web. The Java compiler and a good development system (I like Eclipse) are available for free, and there is a really good free pdf textbook suitable for people who know nothing about programming that covers the most recent incarnation of Java.

There's a lot of hype for Java, and a lot of negative bashing on the net about performance. There is a performance penalty in terms of speed for using Java, maybe 20%, in my experience. There are debunkings and counter-debunkings out there, and my advice is to ignore them- some of the worst knocks on Java were true a few years ago, but the language has continued to improve. Java lets a novice programmer do a lot of very cool things, and there is tons of support available on the Web. Ignore the programmer religious wars about which language is better.

Doing things that take a lot of time in other procedural languages are pretty easy in Java (even though there are C/C++/C# compilers available for free, the learning curve for programming in a GUI environment is pretty steep for these. I have found it much less so for Java).

For me the bottom line is this: I can do neat stuff with Java more quickly and with less fuss than with C++ and the other popular languages that I know about. I have been able to teach myself how to make some cool software in a relatively short period of time, and I can run this software on my Mac and my PCs. Is Java the greatest programming language on Earth? Don't know, don't care. Still, searching for info on Java has led me to some interesting name-calling and fighting about whether Java or C++ or C# is the best or sucks the most butt.

There are some weird things I dislike about Java, and I think I'll continue with this in another post. For the price, you can't beat it.

My very favorite thing is that the Eclipse development environment and Java work the same on my Mac and PCs. I have a PC at work, and a mixed-marriage of all sorts of computers at home, but my primary platform at home is the Mac. OS X runs Java stuff very well. Being able to pick up at home where I left off at work without kicking my kid off the PC is nice.

Musings

2007-05-14T22:33:00.000-04:00

Except for those of us who got hooked early, I think science is a tough sell. There's little money, and the job market is flat (despite years of hearing about shortages of scientists), and there's almost no way the hours one puts in will pay off financially. That's the bad economic news.

Science is hard work, plenty of it boring, in relative obscurity, with a fair amount of isolation. So there is a social downside.

And if you are looking to 'change the world', being an activist or lawyer is going to look like a more direct route. Science is knowledge production, and one has damned little control about how or if it is used. So the impact of a single scientist is going to be limited.

Scientific superstars have a supporting cast that does the work and get none of the glory. So science has a sort of serfdom feel to it. (Worse, there is some sort of quasi-monastic bullshit that surrounds science, that makes people act like the serfs ought to be grateful for their squalor.)

And yet...

It's awesome, captivating, enchanting and mesmerizing. I still can't believe that I am paid to do this, even if paid poorly relative to others who have put in similar time in academia. It was worth the years in school, and the postdoc, and the realization that, in my general field, I could have gotten a BS in chemical engineering and gotten both more money and more respect. But I wouldn't have the ability and freedom to really find things out. In my opinion, there is nothing better.

Chemistry blogs

2007-04-23T22:17:00.000-04:00

Damn, there are some good chemistry blogs out there! I have just started looking, and I have found several that I already dig considerably. Almost all my work in grad school and now, in real life, has been on carbon-based electronics. So I really like this one.

Mother of Invention

2007-03-01T22:42:00.000-05:00

In some sense, working as a chemist in industry, especially working for a company that is very product-focused, I get paid to invent stuff. Part of my job involves developing things that we can patent, and either make ourselves, or license for someone else to make. If, by any chance, this sounds glamorous to you, I want to dispel a myth or two. I would be the first to admit, I do have a cool job that I love. Science is fun, and doing this sort of thing with added economic constraints is pretty charming, too. But the stuff Edison said about the ratio of perspiration to inspiration is only true if you are Edison. For me, the inspiration part makes up more like 0.1%.

In fact, so much dung has to be shoveled to get roses that many people I talk to who start off thinking that science is linear and straightforward advancement towards "breakthroughs" end up wondering how anyone can stand the frustration of having most things not work. I'm not sure what personality traits are vital for science and engineering except one, and that one is absolutely vital: persistence. Persistence and work will cover a lot of sins.

When I was a kid, my dad got me a book one Christmas called Inventing for Fun and Profit by Robert Lay Hallock. I don't remember much about exactly what sort of inventions Hallock talked about (drywall fasteners and ice trays, maybe?) but he did a pretty good job of representing the iterative nature of invention. You try, try again, because at first, you won't succeed.

I think that a love of tinkering is vital, too. You just need to love to make stuff, and lots of it. You have to love the process, the methods and the intermediate stages as much (maybe more) than the final product.

When I get home, after dinner and family time, I usually fiddle with some project or another. Doing much serious chemistry at home is just not possible. But I am just about as interested in electronics as I am chemistry, and so far, there aren't any laws against that.

Right now, for instance, I am working on a light system for my nighttime walks and jogs. Yes, I could buy a light for less than $10. Were you not paying attention above?

I am using an accelerometer chip (pictured here, it is the little square device). I designed the board myself using free software available on the web (here). The accelerometer can sense the motion of my body as I walk or jog, and turn on the lights. If I can get the software just right, it will not turn on the lights without me doing fairly purposeful motion. The software resides in a little 8-pin microprocessor (PIC12F675, for anyone who cares), and I am writing the software using a free compiler I got online (here).

All the software tools I am using were free. The accelerometer was a free sample, too, as was the microprocessor. I bought the programmer I am using for under $40. The resources that are available on the web for the taking are amazing, and they make it possible to do many sophisticated things that would have been expensive or impossible a decade ago.

The board I constructed using a laser-printer toner transfer system, where a specially coated paper is printed with the design of the circuit board. This is then laminated onto a copper board, and the excess copper etched away. It takes maybe half an hour from printing to being ready to solder.

Soldering is a skill that it takes some time to master. Someone with a lot of skill might see my soldering and be sick- in my own defense, these work and have proven to be robust, if ugly.

Some of the parts I am using are surface mount. If you look at the picture here, you see a row of white-yellow LEDs with little black things underneath. Those black things are transistors, and they are tiny. They'll switch an amp, though. If you notice, I haven't installed the accelerometer on this board as yet. I am using the 'breakout' board shown in the other photo to figure out exactly how the little feller works before committing it to soldering on my main prototype. I may end up changing out capacitors or resistors, and don't want to risk my prototype while I'm still learning.

I still have a lot of work to do, but I have got the main routines written for the microprocessor (it is mounted on the back of the board, but you can see the eight pins on the lower left of the front of the board). I am, as I mentioned, working incrementally. I have fooled with the accelerometer a while now, and am learning how it reacts to walking in a stride vs running vs getting my junk ready to go out the door. Translating this knowledge into algorithms that will reliably turn my lights on and off will take time, and will require lots of head scratching and software re-writes. But I am pinning down one piece at a time, and will get it all to work before too long.

I'm already looking ahead to the Mark II model, which will flash in a different pattern when illuminated by automobile lights. Fun, fun, fun.

No good options

2007-02-18T22:05:00.000-05:00

For most of my life, since about the age of 6, I have worn glasses. I am slightly farsighted in one eye, and somewhat nearsighted in the other. I have a lazy eye that wants to turn in a bit.

I went without glasses for a couple of years in my late 20's. My nearsighted eye was pretty close to normal, and I could compensate for my farsightedness. Reading and driving was no problem. But after a few years, it became tiring to compensate, so I got new glasses. I wore them every day for 10 years or so.

Last week, I went for a visit to the optometrist, because I had noticed my vision slipping a bit. Very much so when I work up close, which I do when I build electronics and prototypes of instruments. At least a few days a week I would be crossed and headachy after struggling to see something small.

What the doctor found was that with both eyes corrected, the two 'fight' to the point that my glasses actually make things worse. Wearing glasses makes my vision worse, by correcting the problems in each eye.

So he suggested going without, and using the farsighted eye for distance, and the nearsighted eye for close work, with a magnifier for little stuff. This works surprisingly well. I am going to wear one contact, on the nearsighted eye, to help with driving. But for now at least, there's just no point in correcting my sight.

It's 12:00 somewhere

2007-02-08T18:01:00.000-05:00

As products have increasingly powerful computing embedded in them, the possibility emerges that things will actually become easier to use. Fifteen or so years ago, some of us laughed at the technically-challenged, who could not program their VCR, and so forever lived with a display stupidly blinking 12:00, and who could not access the super-uber-elite timing and show-recording powers locked away for only those familiar with assembly language, calculus, and the grammatical salad common in manuals of the day (and, alas, to this day. Is it really impossible to hire an engineer with even a rudimentary ability to write? The bar is pretty low, as poorly as many manuals are written.)

Complicated tools can be perfectly appropriate for complex, demanding tasks, because there is a net improvement in productivity that pays back the effort in mastering the tools. Now that I have grown up a little, it occurs to me how stupid I was expecting anyone to struggle to master a complicated tool that was supposed to help them do something simple. A Masters degree in computer science is a little much to expect someone to undertake just to record Magnum, P.I.

Those of us who “got it” usually did so as a spillover benefit from the other technically challenging things we did- majoring in chemistry and math meant I might have a little edge in deciphering complicated things, I guess. (Taking economics had the spillover benefit of allowing me to drop fancy phrases like “spillover benefit”, so perhaps my electives were not a waste of time after all).

I have a printer for my home network that came with a poster telling how to set it up. When I upgraded to a new computer, I had long since forgotten about the poster. I just needed to plug in the USB cable and load the driver, right? How hard could it be?

Several hours hard, that's how. I thought I would lose my mind, fling the printer out the window, along with the computer, and go on a multi-state shooting spree before finally getting the damned thing to work. I'd love to send the design team responsible for that fiasco a full-sized picture of me drop-kicking their printer while giving them the finger. After a while, it dawned on me that I might need to install the drivers first. This turned out to solve my problem. The printer is great, but there is no excuse for the way it has to be set up.

Whatever point there was to making things so obtuse, it is still true that this is a stupid way to do things. Almost everything I have used that has a USB connection queries you for the driver the first time you plug it in. What did I get for all my trouble? Other than hundreds of megabytes of other software I have never used? Whatever it was, the particular manufacturer has made a believer out of me. I now believe firmly that I will never buy anything from a company that violates the rule that a customer buys a product for the benefits it confers, and is not interested in doing half of the engineering necessary for getting the benefits he or she paid for.

I help create things that will be in products that people will use, and know how hard it is. Yet I also remember that it is people not unlike me that will someday have to use what I make, so I try to remember to aim at sparing others the pain that I have endured. I want things to work for them, for my small contribution to the world to at least not add to their aggravation. If I can make something exciting, and delightful, all the better. But just not pissing them off would be a cut above much of the rest.

Out of the Closet

2006-12-15T23:17:00.000-05:00

Some people think that I am a Republican. I think my dad thinks this, and might be a little worried that I have fallen under the spell of Neocons and fundamentalist Christians. I oppose any government suppression of free religious expression. I am suspicious of government programs and regulations, and I have peculiar ideas about economics for a son of a former union member. Not to worry, Pop. I'm not Republican. (Not that there's anything wrong with that. Well, no more so than other common alternatives).

Others incorrectly assume that I am a Democrat, because I am pro-science, a staunch defender of medical research, and of teaching biology properly with evolution at the core. I am against the military getting too powerful, and I am suspicious of corporate power. I oppose religious intervention in government. But I am very much not a Democrat. (The same NTTAWWT applies here.)

I am libertartian. Jeffersonian "that government that governs best, governs least" democrat-republican libertarian. The actual Libertarian Party I know very little of, and I suspect it might be full of loonies, but I don't know, so my apologies to any card carriers if I have this wrong. In past times, I would have been called a Liberal, and later, a Classical Liberal. The term 'liberal' has been debased somewhat, at least in the 20th century in the US, and has now fallen out of favor for those who now call themselves 'progressive', so maybe liberal can go back to meaning, well, liberal in the Enlightenment sense of valuing individuals, their freedom, initiative, energy and property, as opposed to expecting collective solutions to problems, but to avoid confusion, I'm afraid that term is off limits for now.

I have had it patiently explained to me that libertarians hate everyone, are selfish, impractical, and are largely misanthropic, tin-foil hat wearing dupes of capitalism that want everything in private hands. These are the nice things 'liberal' people say. Republicans are more often willing to admit that I might have a point, but think that libertarians are atheists and dope-smokers who really want to be Republicans, but lack the moral fiber. While I support people's right to intoxicants with responsibility, I also support their right to religion with similar responsibility. And I don't need lectures on morality from Republicans, thank you.

I support individual liberty, property rights and freedom. To a large extent, both Democrats and Republicans have reservations about these. I hope to say more about this, though this will never devolve into a blog about politics. But for now, I just needed to come out.

Sirens of Titan

2006-12-15T22:37:00.001-05:00

This is Titan, Saturn's haunting and and mysterious moon. Titan is arguably he most fascinating place outside Earth in our solar system. This image is just stunning, in my opinion- more so even than those of Mars, which rightfully garners a lot of attention. Titan is an active, vital object, a "somewhere" outside Earth we instinctively recognize as a world. A world that beckons us to explore. A world frozen and hostile to us, no doubt, with lakes of liquid methane and ethane lapping on frigid shores.

Still, Titan alive in a way our own moon is not. The Cassini-Huygens mission is quietly producing exciting and compelling science, and the results are worth a look. You can find more here.

Titan is the second-largest moon in the solar system (behind Jupiter's Ganymede, which is pretty boring and barren by comparison) and is larger than any of the dwarf planets. It is the only moon with a dense atmosphere. The clouds may be made of ethane, and the lakes, though not absolutely confirmed, seem to exist near the poles, and are probably hydrocarbons. As a chemist, I find this particularly exciting. Titan is clearly cold, and hostile, but with all that organic material, something interesting is going on, perhaps supporting a primitive form of life.

Pressure Cooker

2006-12-09T21:15:00.000-05:00

I have not written anything here for a while because I am part of several projects at work that consume most of time lately. I spend most of my free time with the wife and kids as much as possible.

Which set me thinking- why do people go to school for decades, study really challenging and frustrating things, and then go get jobs that take over their lives?

For a scientist, I assure you it isn't the money, even in industry. I love what I do, but I still wonder at how hard I work sometimes. It comes from something other than ambition, and other than love.

The best way I can describe it is obligation. Part of the training that I received instilled a lot of discipline and tenacity when attacking problems. It is necessary to have these attributes to get anywhere in research, no doubt. But still, because I am a scientist, I feel like I have to work in a sort of single-minded, grinding way, whether the project warrants the effort or not.

I am not complaining. My work is interesting, and certainly beats most other things I can imagine doing for comparable remuneration. But there is something there that seems less than rational.

I especially see it in academics- they get paid much less than industrial scientists, and work really hard, especially at first in order to get tenure. Once that hurdle is cleared, though, the pressure remains if one wants to remain active in the field. Certainly, some do not, and languish happily, knowing they can't be fired. But if you aren't excitied by what you are doing, it is stll an incredibly uncertain road to a job with very poor reward in comparison to the effort expended to get there.

Some academic friends of mine claim that the freedom that they have is the reward. I think this is demonstrably nonsense, part of the bullshit that they tell us as we join the club; most of the time, they have to work on what they can get funded. Their freedom is fettered, and their time squandered by service obligations and office hours. They direct their own research quite a bit, but do almost none of it, leaving it to grad students that impose yet another burden that must be funded. Foregoing a little of this 'control' could return much more financial reward, while also yielding the existential pleasures of actually getting to do some of the science.

Usually, I have almost total freedom in how I proceed, even when my choice of project is not entirely my own. In any case, I find my work interesting, and do not chafe at the few restrictions I encounter. Unlike my academic friends, if I want time in the lab, I just go there and work.

Part of the reason scientist think this way is that the 'scientist club' only fully accepts academic scientists. Anything less than getting a tenure-track job, then tenure, is a kind of failure. Utter bullshit. But the culture of academic science, which is where we all start, assumes that only academic science counts, and many of us who took different paths have a hard time shaking this, too. Having seen both, I know work coming from each spans the gulf from sublime to ridiculous. If anything, selective pressure is worse in industry, because there the science has to work well enough to make money. Much good science gets killed off before blossoming, but what survives is usually rock-solid.

I have been enculturated to work at a grinding pace, nonetheless.

I think I perceive an almost monastic quality in academics- that they must dedicate all their efforts to their discipline, like the medieval monk would turn all his thoughts to God. To do less is to be less. To not suffer in relative poverty is to exhibit something unseemly, as if ambition and success are sins. Many academics act as though money taints, and poverty enobles. That's bullshit, mind you, but that's what I hear them say, and watch them demonstrate.

I have more to say, especially about how limited I think the worldview of science has become, but I want to think more about this first.

Power

2006-10-29T00:26:00.000-04:00

One of the reasons that I love science is that it gives me the power to do things. It is probably one of the things that attracted me to chemistry as a kid- the ability to make things explode, burn, gel, polymerize, change color- all of these have a visceral appeal to them.

I was a kid when computers first became available to individuals. There is no doubt that I fell in love with them for exactly the same reason.

What makes chemistry so hard is not that there is any one part that is beyond the comprehension of an idividual of normal intelligence, but that the subject is so vast and interelated that it is difficult to get a hand hold in the beginning. And frankly, what one learns in the earliest formal class in chemistry doesn't give one much ability to do things. It gets a little better in organic chemistry, the power yield, but the input in time, and the necessity to master a daunting array of facts by internalizing a handful of powerful organizing principles escapes many, if not most, students. But this is what is necessary to use chemistry to do things.

Computer programming, when I was a kid up through college, was similarly daunting. I learned Basic, then FORTRAN, assembly, then C, then C++. Each new project was begun anew, though I learned to save my earlier work.

Paradigms began to emerge in computer science that conspired to save prior work and coding. The use of libraries of code meant that once something hard was figured out, one could include this work in new programs. Changing and extending this could be problematic, but it was very much an improvement.

If libraries of code were designed well, the person using them did not need to worry about how they worked.

This continues to this day, with the advent of programming models such as Object Oriented Programming. This took some time for me to understand, but the benefits were clear- when designed well, it allowed even more code reuse, less worry about how the implementation was done, but significantly, it allowed one to 'grandfather' in earlier code, using inheritance, to make a new variant of the code that extended or changed the original without doing any modification to the original directly.

There is a similar seismic shift in Web-based programming. We are in the early phases of this, although web applications are available that have the functionality of desktop apps (Google's Spreadsheet and Wordprocessing applications are examples. You need a Google account to get to them, but that is free, as are the apps.)

It is particularly easy to use some of the resources available on the web- Google, Yahoo, Amazon, and others are providing application programming interfaces (APIs) to their services. This allows someone with very limited programming experience to leverage the work (and servers!) of these companies to accomplish goals in their own webpages.

Both Yahoo and Google have map services and provide APIs for them. With just a few lines of code, I can (for example) bring up a map of the National Zoo in Washington DC. All the work to find and display this data, to say nothing of the expense and work that went in to gathering and entering it into computers, is available to me free of charge. The force multiplication is hard to imagine.

Blogger, unfortunately, doesn't seem to allow javascript in entries, or I'd show some. I have begun to set up a server at home, and I will link to stuff I do in the future.

Think Different

2006-10-16T00:41:00.000-04:00

I recently bought a Mac. I use a PC every day at work, and haven't really fiddled with Macs much since I was a computer system manager at a commercial printing company in the early '90s. I wanted a new computer, and thought long and hard about the new Intel-based Macs. I'd like to be able to say that I made the decision rationally, but actually, I gambled that the new Macs would just be cool.

I have not been disappointed. There have been years of fighting back and forth between Mac and PC users about which is the best. I'm not going to go there, except to note a few things.

Macs are easier to use. While I have not encountered anything that I simply couldn't do on the PC that I can now do on the Mac, most of what I have done has just been easier. I have downloaded only one driver, and yet I have connected my camcorder and digital camera, and every other thing with a USB or firewire port on it, to the Mac. Worked without any fuss. I was able to do this with my PC only after installing drivers, and fussing. I think I am pretty much at the top end of computer literacy (about half of my professional work involves writing software), and am frankly amazed at how easy setting up the Mac has been.

The Mac OS X is based on Unix. So automatically there is a crapload of free high-quality software available. I use OpenOffice for basic productivity work like word processing. Free. High quality. I have set up Linux on a handful of computers over the past few years. OS X is far, far easier to manage. Not to cut on Linux, because I love it. But OS X is far less fussy.

Development tools are FREE. You can get crippleware versions of Microsoft's development tools for free, but their professional-level tools are very expensive. You have to sign up for Apple's Developer Program, but this is free, and then you can download their development tools. The real stuff. I have been programming in one capacity or another for over 30 years. The process has become quite involved for modern operating systems. The Apple tools are as good as I have seen.

Overall, from the point of view of a computer user, the Mac is great, a very empowering tool. From a programmer's perspective, I am still in the early stages of finding my way around, but what I have seen so far is phenomenally good.

I like my PCs, and there are places where industry software is more available for the PC. I have a lot of programming that I do that uses a plain old serial port, which the Mac lacks (though it could probably emulate this using the USB port). And the model Mac I have doesn't have slots that I can insert interface cards into (though, again, most of the stuff I want to do with data acquisition can be done via USB port these days). On the other hand, my Intel Mac can boot Windows if I need it too.

Hey, y'all look at this...

2006-10-02T07:55:00.000-04:00

One thing that has sort of hung over the success of Apollo !!, the mind-bending historical high-water-mark for human technology, is that Neil Armstrong gaffed his lines when he stepped on the moon for the first time. It is telling that this is what people seized upon. And what it tells isn't pretty.

After all these years, it appears Neil was right when he claimed that he had gotten it right. Sophisticated audio analysis found the 'a' in his famous phrase, "That's one small step for a man, one giant leap for Mankind."

Since there are loons that think we never actually went to the moon, I am certain some people will not believe this, taking some sort of bizzare pleasure in shitting on one of mankind's (and frankly, Neil Armstrong's) accomplishment. This will continue to reveal the ugly, petty side of human nature.

If it were me, I'd have been hard pressed to not say "Lookit me, I'm on the goddammed moon!" People would still be talking about that, but there would not be any ambiguity.

Predicting the future

2006-09-30T17:55:00.000-04:00

People are awful at predicting the future. When I was a kid, in the 1970s, I heard all sorts of predictions- that the world would end at any day (I grew up in the Bible Belt), that communism was destined to rule the world, that the heyday of the United States was in the past and we would soon decay away. I heard stories that we would soon run out of oil, that nuclear energy was the future, except that there was no future, because the US and the Soviet Union would soon destroy Earth in a nuclear war. I heard predictions that bellbottoms would return. And that we would have a colony on the moon by the year 2000.

Scientists are as bad or worse than any of the rest. While they may know one particular area very well, it is the interactions between areas, and the unexpected developments, that really drive science. And many scientists, some of them brilliant men and women that I know personally, are just butt ignorant of even the basics of economics and sociology. There a forces, therefore, that they never consider, and as such, their prognostications are pretty well useless.

So I tend to be pretty dismissive of predictions, especially very specific predictions. Worse are policy suggestions that come from scientists.

Still, I expect progress, and I expect more progress than I "expect". Most progress that we forsee is some linear application of new technology, or some extension of well-tested theories. I expect that some especially sagacious scientist might be able to predict forward a year or two if the predictions are sufficiently circumscribed, but I think that the scientist would also have to be damned lucky, too.

No one predicted the way the internet has taken off. Far more importantly, no one could have planned the internet. If someone had set out twenty years ago to create what spontaneously arose out of the skeleton net that government, military and academia had put togetther, we would not have it today, and it would not be essentially free to access. It grew a little at a time, with each advance adding new and unforseen possibilities. It could not have been planned, because it was invented incrementally. Surprisingly, there is actually a handful of scientific principles that explain why technological innovation is diffcult to predict.

These principles not only explain the lack of predictive success in science, but also in politics, especially the sort of activist politics that characterized the golden age of centralized planning in the early to mid 20th century. They suggest that careful central planning of anything complicated is doomed to failure.

An analogy might help illustrate one major principle: Imagine reaching for a glass of water. You don't plan the trajectory in detail- you simply set the goal. The mechanism your body and brain use to accomplish this is one that involves a constant monitoring of the position of your hand, and successive minor adjustments designed to minimize the error between the position of your hand, and the position of the glass. The monitoring of the error signal is known in control theory as feedback.

You might think of feedback in more colloquial terms- basically someone giving their opinion of what you are doing. This can count, if it is used by you to adjust your approach. Or you might think about the horrible squeal that the PA system at PTA meetings makes. That is a kind of feedback, but instead of helping by minimizing errors, it squalks because it maximizes the error. Oddly, such feedback is called "positive feedback" because it adds to the error. The good feedback, the error signal monitoring that allows you to pick up you water glass, is negative, because it chips away at the error signal until you succeed.

Suppose, instead, you carefully planned the exact 3 dimensional trajectory in space that you would take before you stared. Suppose that, as you approached your goal, something either got in the way, or moved the glass. You would, in real life, automatically adjust, but that's using feedback- if you used only the pre-planning, you'd never reach the goal. It is tempting to say that government is different from that. It is when it works. But the "glorious 5 year plans" that failed communism so profoundly were clearly of the opposite character.

So it is difficult to plan your path, though vital to plan your goal. Actions are determined by feedback, and what actually incarnates in the process, a surprise.

Another thing that makes prediction of the future is nonlinearity. When something has a nonlinear response, the reaction to a small change may be wildly out of proportion. Weather is the classic example. But consider the invention of integrated circuits.

When I was a youngster, a Cub Scout I think, I saw a minicomputer on a field trip. 'Minicomputer' meant that it only took up about a third of the office it was kept in. It was boring- a big box used by an accounting office. No indication that within a few years, the exponential advances in integrated circuitry would mean my best friend would own an early microcomputer, and that within a few decades, I would own more computing power sitting unused in my garage than existed in private hands at the time I saw the minicomputer. There was no display obvious in the minicomputer room. I think it was programmed via punched cards, and its read out was a big line printer. I recently installed a graphics coprocessor for my son that is as powerful as any computer I had owned as recently as a few years ago. Exponential changes make things cheaper and more powerful at a rate that is difficult to fathom, and impossible to predict.

Exponential vs linear growth is something that is hard to wrap one's mind around. Imagine the increases in your paycheck over time. Linear with time, if you are lucky. We intuitively understand this. We understand getting double out when we double our effforts.

Now, imagine bacteria introduced into a bowl of beef broth, a single bacterium. Soon there are 2, then, in the same span of time again, let's assume 1 minute, 4. This continues, and, if you only notice the growth at the very beginning, it doesn't look much different from linear growth. But 4 becomes 8 becomes 16. Clearly it is fast, but it still is hard to get a sense that it is getting faster, and it is getting faster faster, and getting faster faster faster... Not to belabor the point, but for truly exponential growth, there is no end to the "faster's" that you can concatenate.

After 10 generations we are up to 1024 bacteria. Is this a lot more than if the population increased linearly? Let's compare a linear growth rate, assuming we added 1000 bacteria a second. At 10 seconds, linear growth would give 10,001, while exponential would give 1024. Not impressed with exponential growth yet? Let's wait another 10 seconds. Now we have 20,001 bacteria in the linear growth pot, and 1,048,576 in the exponential growth pot. Hmm. It is tempting to stop here, but remember, not only the rate, but the rate at which the rate increases increases with time. 10 seconds later, the linear pot has 30,001 bacteria, while the exponential pot has 1.07 billion.

Okay, you say, so what? Consider that this is exactly the way that compound interest works. If a person begins saving money at a young age, at a modest rate, with a modest rate of return, they can absolutely retire wealthy. But almost no one does it, because we are so poorly tuned to see exponential opportunities. If social security was actually put in a safe treasury bill account, rather than being treated as free money by politicians, there would be no solvency problem.

The brakes eventually are put on our bacteria by limitations to the amount of food and space available. In the world of ideas, it is more difficult to see where natural limits exist, though they may. For the time being, we are in an exponential growth phase of human knowledge, especially led by technology. We have begun to see the limits to miniaturization, because the size of atoms is a wall that we will not be able to breach in any foreseeable way. But then, foresight is not all that good.

There are dark sides to this, and unfortunately, they are equally unpredictable. I don't mean to paint the future as carefree because technology advances so quickly. But I expect that what I worry about now will not end up being the problems that I or my children actually have to work frantically to solve. That is the closest to a good prediction that I can make.

Homeschool Science

2006-09-30T13:08:00.000-04:00

My son approached me the other day asking to be homeschooled. I quizzed him about why he did not want to go to regular public school. Anyone who has read my earlier posts know that I hated elementary school. But I wanted to know what his beef was. Were bullies after him?- if so, we could solve that. What made him uncomfortable?

He said "School science sucks."

Boy, that brought back a flood of memories. He related that most of the time, they either learned words about science, or wrote essays. All of that seemed fine, and I told him that communicating about science was, in fact, a big part of real science. I asked him to describe the experiments that they were doing in his class. It wasn't pretty. Composting and looking at rocks. I began to see the problem.

I support public schools. I think that a basic education is an absolute must for citizenship and a productive life. I support the rights of parents to send their children to religious or charter schools, or no school at all, if they are willing to prove though testing that their children are learning. Still, no matter how ardent a libertarian or conservative or religious one might be, one should be able to see, if the education provided by the state does just the basics, the spillover benefits to the society at large offset considerable costs.

But that is a big "if". Testing suggests that this is not being achieved, especially in the areas of mathematics and science. Still, the public school system in the United States is hideously unresponsive to outside pressure, but it is too important to abandon entirely. I am not pretending that the prevailing culture is something that I always like, but it is the culture we have, the one my kids will have to learn to live in. Finally, I don't think America could survive if we lacked public education- we cannot count on people taking it on themselves to educate their children, and the consequences of not having them educated, even at the present sub-par level, would be dissolution of society.

Put another way, stupid people will make stupid decisions, including electing stupid people. We are already far enough along that road. So I don't feel right about giving up on public schools altogether.

At the same time, I am not willing to abandon my children to a system that will fail them in areas I hold particularly dear, and that are demonstrably important in the modern global economy.

As an experiment, I have begun a modest program of 'homeschooling' my son in science and math. I have an advantage over most parents in that I am a professional scientist, and have knowledge and access to resources that most would not. Over the next couple of weeks, I plan to detail what I am doing and what resources that I have found that are readily accessible. It might help as a guide to parents who are concerned that despite the sloganeering, their child might indeed get left behind in math and science.

Our first science project, as a example, is breeding fruit flies. There are plenty of experiments that can be done once a population has been established, from physiology to behavior to genetics(and for flies, fruit flies are tiny, clean and cute). 'Establishing a population' is a 10-dollar phrase for letting a banana get overripe and trapping a bunch of flies in a babyfood or olive jar along with a chunk of banana- the level of effort past that depends entirely on what you want to do. Just watching what the flies do is an education, if done carefully. Resources abound, from the simplest instructions for care and breeding to detailed, 3-dimensional maps of the animal's brain, most available for free on the web.

The average homeschool mom or dad might have no idea where to start. I want to offer encouragement- there are curricula and guides all over the internet. There are introductions for those who know little or nothing about the subject- to a bigger extent than one might think, that is the case for me when you get too far outside chemistry. There is lots of support out there, and a lot to learn. There is nothing more bond-forming for a parent and child to learn something together, so jump in, don't pretend you are an expert, and have fun figuring stuff out. Which, at its heart, is what science is about.

Assuming Facts Not in Evidence

2006-09-24T01:36:00.000-04:00

I enjoy reading work by Sam Harris, and his recent book The End of Faith is another good piece of writing. In it, he really opposes liberal religious thought as much as fundamentalism. His point of view, that religion is either fundamentalist or intellectually dishonest, is not one that I share, but I see his point.

I won't argue in depth here- I have written recently about my hyper-liberal agnosticatholic stand. And I'll point to a good blog interview with Harris here . There are many other resources that outline his point of view, including his own website. And his book is good.

However, one of his positions, that the world would be better off without religion (one he shares with many others, like Richard Dawkins, to point out a vocal proponent), is particularly curious. There has not been such a time in human history, so the argument is strictly hypothetical. And it isn't clear that rationality is adaptive in the long run, since human beings have only recently embraced it in the distilled form Harris advocates. Because harm comes from part of human nature, it is tempting to assume that it needs to be fixed, and that it can be fixed. It is an assertion made in the absence of evidence, and as a hypothesis, it works poorly, because we are not likely to see such a world.

I am reminded a bit of the arguments of socialists and communists about utopias that would result from dictatorship of the proletariat as being the eptiome of a scientific approach to history. Well, I won't argue the merits of their case for socialism, but I would point out that predictions were not borne out, and eventually, intellectuals on the left largely quit referring to the Marxian ideas of historical inevitability or scientific socialism. They assumed certain results would follow, but the experiments came out differently. So they abandoned the science for the weaker broth of 'political commitments'.

I think that human beings are stuck with a neolithic mind that will automatically generate schemas for understanding the world that are at least quasi-religious. Fighting this is futile, I think, and the best thing one can do is fill these slots with something- liberal religion, secular humanism, but certainly not nothing- as innoculation against something virulent (say, communism, scientology, or fascism) from getting in. Argue with many militant atheists for long, and you will be papered as irrational, stupid and unrepeatable things because you do not hew to their version. One might throw off some religion, and eschew the term, but I think the deeper tendencies die much harder.

My larger point is that it isn't a proven fact that humanity would be better off without it. No one would die for religious reasons, but this is not a guarantee that extremism would no longer take lives. It is too much to believe, absent evidence, that war and murder are going to go away. Where religion was used to justify them, something else will be used. A reasonable scientific question is what adaptive adavantage religion confers. It is so very deep within us, that it must be a manifestation of something useful.

The awful truth may be that being always on the verge of killing one another and believing in fantastical beings was important to human survival. If it had been counteradaptive, would it have survived? And if it is so deeply embedded in us, is it possible or desirable to get rid of it? I wonder.

There seems to be the tacit assumption that atheism would lead to the sort of liberal cerebral temperament that intellectuals in the West embrace. I am not so sure- I can see a certain measure of the western intellectual tendencies toward liberality is quite circumscirbed. In a recent editorial, Harris himself points out that many liberals in America think that militant Islam is less of a threat than the president, and he takes them to task for it.

I think that the idea that the world would be better off without religion sounds good. Reasonable, even. But it isn't necessarily so. Irrationality abounds, is central to the human condition, and the quixotic fight against religion, especially attacking those who are in the best position to moderate it, is clear indication that Mr Harris himself is not immune.

Dead Ends

2006-09-15T20:25:00.000-04:00

Some of the best fun I had in grad school was following up on some unexpected results along the way. In many cases, things that don’t work are merely dead ends. It can be especially vexing if something that “ought” to work craps out. Many times, you just recover starting material- it’s as if you are asking your molecules to do something that they politely decline to do. Sometimes, something does indeed happen, but not what you want. You can often learn from this how to tweak conditions to get your desired product. If it sounds time-consuming and painstaking, then I have described it appropriately.

I was trying to make what looked like a very simple compound using a really simple, straightforward route. Ha. This is something only a new graduate student could say without tongue firmly in cheek. You try the obvious things, and you might even expect them to work. But to think that anything is simple and straightforward the first time you do it is a mistake.

The molecule, and the starting materials I used, are represnted below. The reaction is written backwards; this is the customary way of saying this is what I plan to make out of these other things.

We call this diagram and mode of thought 'retrosynthesis'. What we mean is that if we combine the stuff on the right side of the arrow, in the the right solvent at the right temperature and for the right amount of time, we ought to get the molecule on the left.

I didn't get the molecule on the left. For days, it looked like I got nothing. I would run an analytical technique call gas chromatography/mass spectrometry- if you watch the TV show CSI, they use it all the time, and get completely unambiguous results in a few minutes. Yeah, right. I did the analysis on a drop of reaction mixture taken from the flask, and I'd see my product in the analysis, or at least the results were consistent with the product I wanted. But when I tried to isolate the compound, I got almost nothing. As I said, it isn't surprising to get either starting materials, or some product you do not want. But my results didn't add up. The analysis said what I wanted was the only product in the mix. Yet I recovered almost none.

As an experienced scientist, I would now roll with this. I might be a little frustrated, but I wouldn't worry. Sometimes things don't work that look like they should. Sometimes weird stuff happens. But as a new graduate student, any serious difficulty had me questioning my intelligence, competence and sanity.

The obvious guess was that I was loosing the product in the isolation step. This is pretty easy to do- often separating components of a reaction mixture is difficult. And if the molecule you want is fragile, this has to be taken into consideration, or you can easily destroy all your hard work. But it was frustrating. Each time, no matter how I varied how I did the reaction, I'd see analysis that suggested that there was nothing but what I wanted in the pot, but when I isolated the single component, however careful I was, all I recovered was an absurdly small amount. What the hell?

One day, I was running the GC/MS, and the instrument had been slightly reprogrammed to work a little differently from the other times I had used it. The conditions were the same, except the instrument continued to run for an exended time, for around a half an hour, so there was not any reason to go back to the original program. The target compound I wanted came off the instrument and was recorded at ~6 minutes, just like it always had. The output of the instrument is line with peaks that appear when molecules pass through it- gas chromatography separates the compounds based on how quickly they pass through a capillary coated with something designed to sort molecules by size, or polarity, or other properties. I thought I had one compound because the GC trace had one peak. A sample GC trace is shown here, though not of my compound. Each peak is from a separate compound in the mixture, separated by the time it takes each of them to make it through the capillary:

Associated with each peak is a mass spectrum, a recording of the masses of fragments of the molecule. A sample for the molecule dodecane, a straight hydrocarbon chain is shown below. The fragmentation pattern is essentially a fingerprint for a given compound, as long as the instrumental conditions are reasonably similar.

This can tell you the molecular weight of the compounds separated by GC. My compound of interest, who came out of the GC portion of the instrument at 6 minutes, has a mass of 155. This was another reason that I thought I had the goods, because this matched the MS results for my peak. On the extended run, at around 25 minutes, off came a much larger peak. The relative sizes of peaks in a GC trace tells you the relative amounts of compounds in the mixture. So part of the mystery was unravelling- I had something else in my mixture, apparently making up the bulk of the reaction product. When I checked the mass, it was 310- twice that of the target.

The pattern of little lines in the MS was telling, too. Chlorine has more than one isotope that exists naturally, one a bit more massive than the other. Two major isotopes exist in nature in a very specific ratio, and any compound containing chlorine will show a pattern in the MS that reflects this. This also gives a way to know how many chlorine atoms are in a molecule. My peak at 6 minutes showed a molecule with 2 chorine atoms, just as expected. The peak at 25 minutes was from a molecule with 4. I began to think that there were two of my product coupled some way.

It still didn't explain why I was getting no product to speak of, even the wrong product. Again, I feared I was loosing the product during isolation.

I went back to my flasks. A by-product of the reaction diagrammed above is the combination of the displaced bromine (Br) atoms, and the counterion of the sulfur, which in this case was sodium ion, Na. Counter ions are important, but in chemical reaction equations or retrosyntheses, we often leave them out because they rarely get involved directly in the reaction. So in the reactor, I had what I assumed was a bunch of NaBr, sodium bromide. This was expected. I just decanted away the solvent, expecting it to contain my product. NaBr is soluble in water, like NaCl (or table salt). I figured I would dissolve away the salts, the try and recover any other stuff that formed in the reaction. To my surprise, the salt did not dissolve away. A little fiddling, and I realized I had some organic solid. Perhaps the mysterious molecule of mass 310?

I could not find any solvent that would dissolve more than a trivial amount of the solid. This is an unfortunate fact in chemistry- lots of things are insoluble, and when they are, this fact limits the kinds of analysis and further chemistry that you can do. Still, something dissolved enough to show up in my GC/MS spectra. I needed further tests to figure out what it was.

I found that benzene would dissolve it a little, so I boiled the residue in benzene for a while, and it did dissolve. As I cooled the solution, little hexagonal plates of something began to crytallize out, shimmering little sparkles flashing as the compound fell out of the benzene. This might be my mystery compoud. I knew that getting crystals would allow me to have xray diffraction done, which could definitively tell me what I had. When I gathered up the crystals and weighed them, I was even more excited, because a lot of the missing material that I could not account for had been accounted for by finding the molecule that I had mistaken for salt. The leftover benzene was sent through the GC/MS. One peak, at 310. I ran the thing for several hours to make sure there wasn't a later surprise, but nothing else showed.

Since I had several days that would elapse between giving the crystals to the crystallography and getting back a structure, I sat down and drew what I thought it might be, if it was indeed my mysterious mass 310 product. I imagined various ways of coupling two pieces, but most of the ones that seemed likely would not quite give the right mass. The one that fit the best, I thought, was a 10-membered ring shown below.

There is a lot of lore in chemistry about the likelihood of forming anything other than 5 or 6 membered rings. Smaller rings are too strained, and the ends of molecules that could form larger rings flop about so that they'd never find each other and couple. So this molecule seemed fishy. Still, it fit.

A few professors I showed it too just shrugged. They didn't think it was likely, but not impossible. In any case, the data would come back and I would know. One professor declared that it was all but certainly NOT a ten membered ring, and spent a couple of hours proposing things that I had already considered and rejected. Including the idea that the molecule dimerized in the GC/MS instrument. Perhaps it did, but this didn't explain the pile of hexagonal crystals that formed in my flask. One last adamant foot stomp from him, and I excused myself politely. I figured it must not be what I thought, so I would just wait and see. I had nothing to gain by getting stuck on one structure, when I would just have to defer to the data anyway.

I got an email telling me the structure was finished. We I got to the crystallography lab, the crystallographer had a grin that told me he had found something he thought was interesting. He pronounced the structure a weird one. The molecule, as constructed from the crystal diffraction data, was exactly what we all thought unlikely:

I confess that my first thoughts were the glee I was going to have showing Professor Know-it-all the structure, because there was no arguing with it. I also realized that this would be publishable, precisely because it isn't what one would guess would happen. The crystallographer knew how few examples there were in the crystal databases (I forget now; it might well have been none). Publications are the currency of science, and the quicker I got some out the door, the quicker I could graduate.

This was a dead end, as far as my main project was concerned. But an unusually fruitful dead end, in that I went back and characterized the molecule fully, and got a paper out of it. And I learned a lot about not thinking that prior precedent is a perfect guide, about using things that go wrong to learn, and about never giving up when there is clearly something interesting or unusual going on.

One reason this unusual molecule could be even more interesting is that it has 2 sulfur atoms in a ring- I think that in the right hands, it might bind to heavy metals, like mercury, and so might be good for further chemistry or even environmental cleanup. The chlorine atoms could be a point at which the molecule could be made soluble, or attached to a support, using pretty standard chemistry. I didn't get a chance to follow any of these possibilities, but now, since it is out there for the person who wants to follow up, I hope someone will. I have had other papers published, but this one is especially sweet, because it came out of nowhere and was completely surprising. For anyone near a good college library who wants to see, the reference is Heterocycles, 57 (12), 2373-2381 (2002).

Expert Opinion

2006-09-14T23:33:00.000-04:00

When I was in chemistry graduate school, I followed a typical program- a couple of semesters of core classwork, a series of cumulative exams, an oral qualifying exam, and then several years of research with the odd course here and there. The purpose of the classwork is to get you to the point that you can understand the scientific literature, and so that you can think analytically and, ultimately, creatively, in whatever subspecialty of chemistry you choose. The focus of the PhD program, however, is a multiyear research project, or more likely, a suite of projects that explore some area or topic, through which you are ultimately able to make an original contribution to your field. The process culminates in publication of your work in scientific journals, and the writing of a dissertation, which is read and used to grill you in a final hurdle, the dissertation defense. This is an oral examination focused on your research. By the time you are ready to finish, you probably know the details of your specialty as well as anyone on Earth, so most people pass without incident. The professor that you work for, your advisor, is unlikely to allow you to get up and make a fool of yourself, because you would be doing the same to him. Nevertheless, there are horror stories.

Mine was relatively uneventful, with the exception that I had pissed off one member of the committee, someone who came in from the outside of our department as required by my university. After the end of the grilling, when I had left the room, he groused a bit, I understand, but was mollified by the people who knew what I had been doing for the past few years. I had stepped on his toes regarding the scheduling of my defense (I had already moved 500 miles away to start a postdoctoral position- I was not able to reschedule. There was some miscommunication, I guess, and I think a Dean had to get a bit ugly with the fellow to get it done. The Dean then let me have it for a while. I had it coming, I’m sure.) In the end, I passed, made a few revisions to my dissertation, turned it in, then had it rejected 3 times by the Dean of the graduate school’s office for a) some of the paper it was printed on, b) some margin violations c) the fact that the new paper was different from the old paper, though both met the university specs (I had a friend FedEx me 6 sheets of paper to finally get this finished. For one single page. I ended up needing them all, somehow.) Finally, it was done, and accepted, and I was granted the degree. Some months later, I got a lovely diploma. My even lovlier wife had it framed.

What does this set of letters signify, PhD? Doctor of Philosophy? I try to be philosophical, but I am a scientist. It seems to carry a lot of weight in court cases, for expert witnesses, for self-help book authors, and is a minimum requirement for professorial positions in academia. I got a job in industry as a research scientist that required a PhD.

I think that there are a variety of ways to parse what a chemistry PhD means- competence, original work, ability to make independent contributions to one’s field. But I like the idea that, ultimately, that it is signalling behavior, in the sense that economists use the term. I would argue that in my research job, for instance, I do nothing like what I did as a graduate student, or postdoc, but the signal that I send- that I am able to do creative scientific work, and the metasignal, that I am generally independent, alert, resourseful and willing to invest a lot of energy into achieving goals- give potential employers useful information about how I can be an asset to them, irrespective of my specific skills.

The PhD education is predicated on aquiring necessary skills and knowledge along the way. By definition, original research is something new.

That isn’t to say that specific skills aren’t an asset, and sometime critical. I would not be a good hire for someone needing a lot of formulation expertise. Could I aquire this now? Certainly. But if it was needed out of the gate, I would be a bad pick. I was not trained originally as an electrochemist, and I am not yet an expert, but my skills improve as I have to use this in my work. I go to conferences, and I read the literature. I would be a good hire as an ‘electrochemistry savvy’ organic chemist. In a few years, I think the transformation will be complete enough that I could market myself as an electrochemist if I wanted to. This transition, too, could serve as a signal.

Unfortunately, the general public gets an entirely incorrect signal from the PhD. There are many misconceptions about scientists, some overly negative, like we’re all godless, morality-challenged Frankensteins ready to do whatever suits us for knowledge. (OK, that’s not that far off in some cases). But even more destructive at times is the opposite suppostion- that we are omnibenevolent braniacs, selflessly seeking knowledge for the good of all humankind, and that we know everything. That we are experts. Not about anything in particular, just experts, and our opinions should be followed as somehow superior.

Depending on what you want to know, my opinions may be superior. Synthetic organic chemistry, especially of semiconductive molecular crystals, conducting polymers, organometallic compounds, and charge transfer salts, I am reasonably aware of the current literature, and I can tell you how to make stuff, and how to make things from the stuff. I’m not doing much of this now, but I keep up with it, and I know first hand how to do it. Stuff I now do every day, I know even better, but I’m not at liberty to discuss this. My opinion is sought and my recommendations relied upon; I am paid to provide expertise and to use it for our business.

Stray a bit from this, to something like drug design, and I am not an expert. I can follow the literature, and I understand the synthetic techniques, but I am not familiar with the details of how and why they make what they do.

Going farther afield, to biochemistry or metallurgy, and my expertise falls off even further. Here, I would have to read a lot to be able to follow the literature, if only because the terms and techniques are ourside what I ever use. Occasionally, a problem will arise that involves metallurgy or entomology (yes, really) and I have to go read a bit to get up to speed. I can learn specifics quickly, and I can learn enough to ask experts to help, which is also really important. But it takes special effort, and I am careful to not trust my judgement until I have had a lot of experience.

If you want medical advice, I’m not the one to ask. If you wonder about studies of a treatement or medicine, I know enough statistics and experimental design to evaluate what is published from that perspective. But I am lost without a lot of background already being provided. I read studies of various medications for my parents, and probably know the studies and statistics as well as their physician, but I am not a physician, and want them to ultimately defer to the doctor that they know and trust. But if they want to know how many people got a certain side effect, or how likely it is, or possible drug interactions, I can extract that for them.

Get outside science, and what the heck do I know? I try to follow current events. In that sense, I take citizenship pretty seriously. I probably know more than average, because I read newspapers and keep up with news. I have a little background in economics, but just a little. But I have no special insight.

It worries me when scientists use their platform to advance extra-scientific agendas. I don’t begrudge them using their voice to make a point or to air an opinion- this is their right as citizens. But if they imply that they know something special because they are scientists, and that they should be obeyed or followed, they step beyond that into behavior that I think is unethical, and all the more so because so much of the population has serious misconceptions about science. It is wrong to use this vulnerability to signal something that is not true, and it is antithetical to the aims of science, in my view.

My advice would be to be skeptical of nebulous claims of expertise, and take with a grain of salt the opinions of an electrochemist about the stockmarket. There are no generic ‘experts’.

Hieroglyphics

2006-09-13T22:40:00.000-04:00

When I was a little kid in elementary school, I was fascinated by the space program. I didn't want to be an astronaut just to fly in space, though. I wanted to be a space scientist. Somehow, I deduced that space science involved Einstein, and to understand Einstein, you had to know algebra. So I went to the library to see if I could figure it out.

I could not make any sense of it at all based on what I saw in the odd textbook or two that was there. The technical books were either far too simple, and said nothing except ‘algebra is very complicated, so we will discuss physics without it’ or were so filled with symbols that seemed to never be defined anywhere. I’m not sure, at this tender age, that I understood that such symbols indeed needed to be defined- I just caught on quickly that I was no Einstein, because I could not just pick up any page of deep mathematics and understand it, completely free of context. I was no genius, apparently, and so doomed to never be a ‘great’ scientist.

Still, with this sobering fact still stinging in my mind, I did resolve that I would understand what these symbols meant, someday. While I shoveled coal on a train or something.

As I look around, I see on top of my computer a page of derivations that I have been working through from Jose’ and Saletan’s Classical Dynamics. I include it here as a scan. It’s really pretty run-of-the-mill calculus; partial derivatives scattered across the page scare some people that know a little calculus, but I think this is something students learn by third semester of college calculus (in the spirit of righting the wrongs I suffered as a child, take a look at the little ‘backward 6’ things- I’ll tell you what they mean because no one would tell me years ago: it is a way of watching the change in one quantity as you vary another, while keeping any others involved constant. There are details to flesh out before you can do it yourself, but this is what it means). Clearly, somewhere between being the child in my hometown library and now, as a mature adult, I figured out what those and many other symbols mean. I want to think back to how this happened.

It wasn’t school. By third grade, I was so horrified and brutalized by school that I dispaired of ever getting anything out of it. I hated school, and it hated me. I got paddled a lot, for offenses as trivial as having an untied shoe. This was not some authoritarian Catholic reeducation camp, or military boarding school, mind you, but the benevolent little public school down the street from where I lived. So I gave up on school.

I learned almost nothing of math in middle school. Not long division or mixed fractions or any of that. Nothing. But I kept reading about how I needed to know differential equations and tensors to understand the important parts of physics. All my favorite authors said so- Carl Sagan, Isaac Asimov, Freeman Dyson, George Gamow- but none of them really offered much help in getting there.

Around thirteen, I got mixed up in booze and pot and self-hatred. Thankfully, just as suddenly, I snapped out of it. I really got in a heap of trouble at school- I routinely antagonized teachers, I slacked and malingered and wasted time. But, ironically enough, the crisis came when the vice-principal of the school thought he would get rid of me by claiming I had been ‘selling pills’.

Absolute nonsense. I had drank a pint of cherry flavored vodka in one sitting at 13, and I had smoked some of the nastiest ditchweed marijuana you have ever seen, but I never sold anything (except hits off a 64oz beer a guy on my paper route gave me in lieu of payment once, but that was outside of school). But I never sold any pills, nor did I take any. It just wasn’t the redneck punk kid idiom then. Dope and liquor. Lynard Skynard and ZZ Top. Pills seemed kinda queer. I think I heard about people taking Quaaludes, but I had no idea what they were, and they didn’t seem appealing.

The moment of truth came and went, because the vice principal could not produce any evidence, nor did he seem to have a clear idea of what he wanted to do. But I got sent to a new school on the initiative of myself and my parents. One with a rough reputation.

To be honest, I cannot remember a thing about it. I certainly didn’t have any mathematical or scientific epiphany then, with the exception that I had discovered chemistry was good for making explosives. This is a story in itself that I will tell later, but is, at its heart, why I am a chemist and not a physicist, and why, though I am deeply attracted to theory, I will always be an experimentalist. Nearly blowing yourself up scares you, certainly, but it is an integral part of the formation of many chemists I know.

I had a short time to reflect, though, about the fact that I was headed nowhere. I laid off the vices- not that I didn’t drink the occasional beer in high school, and I smoked a joint again at 14, but the hardcore self-destruction stopped before it ever got started. I could just see, in that brief interlude, that it led to oblivion.

I went back into the school system that I had escaped- my first year of high school, I figured out quickly that I was right about my assessment of where my old friends were headed (and to a man, they all crashed hard and never really recovered the promise they showed).

By contrast, as my childhood buddies from elementary school went on to high school, they fell in with kids that knew that they wanted to go to college and be something.

I sort of thought that this was bullshit, but as I hung out with them, and transferred back into the better school system (with the rough reputation), I just naturally started to act more like them. I started to want my path to be like theirs. I started to believe that I could do it. They seemed sure they could, and I was frankly sure that I was at least their intellectual equal. I began to regret all the goofing off. I hoped that it wasn't too late to turn around. I feared that my bad grades in high school might keep me out of college. Back to shoveling coal on the train. I really wanted to avoid that.

In ninth grade, algebra had been a bit of a muddle, because I had not paid attention, and figured my chance at being a prodigy was spent, so I’d never be a scientist, so who cared. I could be a ne'er-do-well and badass and maybe still avoid being a coal-shoveler, if not an inmate. All these worries about not being able to be a scientist because I was no Einstein were stupid thoughts, in retrospect. I have met real prodigies since then. Some did well as professional scientists, and some did not at all.

But being a prodigy or genius certainly isn’t a prerequisite for being a scientist, and the horrible hagiographic biographies of great scientists have done a lot of harm by making it seem so. Hell, even Einstein was not the Einstein I imagined when I was a kid, and this is not to diminish any of his awesome accomplishments. Einstein is an important scientist, but not the only one. Not every mathematician has to be Gauss to be good and productive, either.

So in 2nd year algebra, things started poorly. I got D’s several periods. I started off never doing my homework, which is why I got D’s, but I started paying attention. I made a couple of brainy friends, and we got to where we competed at doing the homework. One kid really shone, and I set my sights on him. It became fun. I got good at it. I started thinking about it a lot, asking teachers for extra stuff. I started to wonder about it, to vaguely realize how deep and interesting it is.

My good crowd let me know that I had to take geometry and Algebra 2 at the same time to make it to calculus. Calculus- the word alone was enough to fill most kids with dread. But I needed calculus. I had decided I would be a physicist. I was still getting D’s in math, but I knew that this was not indicative of what I could do. I knew the D's would go away once I started to engage, and they did. Geometry was fascinating, and exposed me to logic in a way that forever changed my way of looking at the world. I could chain ideas together. I could actually, definitively prove some things. There was a certainty to the world that I had never recognized.

I also took intro physics my sophomore year from a kind and gentle man, one so pliant and easy going that we barely got into the subject at all. He seemed, in a way, unwilling to make us learn it. But I asked him about the difficult and mysterious world of differential equations, and he lit up. He gave me a copy of his college calculus book. I looked in it, and with my budding mathematical skills, I knew that I could figure this stuff out. I still have the book- it is still one of my most prized possessions.

The summer between sophomore and junior year, I carried the calculus book around a lot. It was going to solve some of the childhood mysteries for me. First, I was able to decipher a hieroglyphic that had filled me with shame at my ignorance as an elementary school student, the mysterious sigma, the greek letter that looks like a weird E or something.

To hardcore mathies, this has to sound a little stupid. But as a kid, literally no one I encountered had any idea what this thing meant. It might come as a surprise to engineers and scientists that almost none of the nontechnical people they encounter has any idea. I didn’t grow up around engineers or scientists, just good, working-class people that thought I was a little weird but loved me anyway.

The revelation that sigma means to sum, to add up a string of values using some rule specified by what follows it, was like Champollion sitting down with the Rosetta stone and knowing for the first time what was written in Egyptian tombs. I was giddy, and felt oddly powerful, like an initiate into a secret society. I knew something that most of my friends, even those that would eventually become fluent in mathematics, found inpenetrable. I wanted to tell them, but found out quickly that nothing kills a party like a math nerd trying to explain something ‘cool’ they figured out. Mathematics is, alas, often a solitary meal. Still delicious, though. Then, there on page 201, where scribbling from those days when I was not yet 16 still linger, I figured out the fundamental theorem of calculus. I knew what it meant. I wasn’t good at calculus yet, I couldn’t apply it, but I understood what it meant. I understood the proof, and would for ever after know what calculus was about.

I can still remember the surprise in my mind, that I understood. It was afternoon, sometime in the summer, and I had taken another stab at figuring things out. As these things go, there was some critical insight that I had been missing- I have no idea what it was now, but I still go through the same sequence to this day as I struggle with new science and math. With proper tutoring, I would have no doubt sped right past whatever it was that was hanging me up, but I would have been robbed of the joy of having the parts snap together suddenly in my mind. I may have even hugged the book. I let myself have the rest of the day away from the book, just to relish the feeling. I went through a lot more of the book that summer, mainly the sections on applications of single variable calculus.

Junior year was trigonometry for math, and chemistry for science. I fell in love with chemistry. I still had a machismo thing that made physics and math seem like the only subjects worthy of a math-jock like me (sometimes, I still indulge in this, though I know it is patently untrue. I keep the math and physics dusted off to abuse my chemist friends, and for fun. But I have seen what I think of as simple chemistry absolutely dumbfound bright physicists. It requires a different way of thinking. I hope to get into that another day). But chemistry was fun. Trig was fun. I knew where this was all headed the next year in calculus, so none of it seemed pointless. Some of the brainy kids from algebra seemed to fall by the wayside as math required more than the gymnastic skill algebra demands, and began to become deep conceptually. When we talked about infinite series, and imaginary numbers (you use them in algebra, but as a formal thing. Not as a concept.) some never really recovered. I got decent grades for the first time in my life. I began to think about where to go to college more than if I would go.

Senior year calculus was a breeze. I got mainly A’s, even one semester of straight A’s to prove to my girlfriend that I could do it. I whipped several ‘good scholar’ kids in the community at a Math Science League in chemistry. It outraged some of them that a C average kid was even there. It galled the hell out of the principal to have to give me an award for winning. I came in third in math, but I am fairly sure that this is because my computational skills were still developing. I still had trouble with long division and mixed fractions, and was wont to drop a negative sign here and there. Bad habits from my slacking days.

College did not go so smoothly, but I will leave that story for another time, except to catch up to the present, and to say that ultimately, it was a triumph, though circuitous. I have a BS in Chemistry, enough hours in Physics for a BS in physics, a minor in Math, and a PhD in Chemistry. I did a post doc at a physics lab, and have a great job doing industrial research where I get to use a little of all of it, plus a little engineering here and there.

The moral of the story is that the road was personal, and I did what I started out to do as a little kid, though I dispaired of getting to the end of it many times along the way. I owe what I have accomplished to my parents teaching me that I could do whatever I decided to do (deciding being the hard part) and to my grandmother, who told me to never let anyone beat me out of an education, including myself. I wish I had put money on it in third grade when they told me I’d never be a scientist because I had no mathematical ability. Now, I need to stop. I have some differential geometry to study.

Remebrance

2006-09-11T22:46:00.000-04:00

September 11 will always ring in the ears of anyone alive and old enough to be consciouss of what happened that day in 2001.

Let us be clear about one thing: what happened that day was not a tragedy. It was an outrage. The question that arose in so many Americans that day- "Why do they hate us?"- and the myriad answers given, from the studied and reflective to the asinine and ridiculous- speak volumes about the character of this nation. It would be, to almost any other nation, even empire, at any other point in history, hardly given a second thought as the fire of hatred and lust for revenge welled up inside. No Roman openly wished for "a million Cannae's" the way one particularly lame-brained academic wished for a million Mogedishu's. But we cared that someone hated us enough to hurt us in such a brutal and senseless way. We wondered why.

The answer is complex, and still to some degree banal, and I have neither the expertise nor the inclination to answer. I will not deny that the foreign policy of this country has left in its wake many enemies, many who are rightfully resentful and disenchanted.

But we did not "deserve it". The World Trade Center was not full of 'little Eichmanns", working away to enslave and destroy. I'll save my pro-capitalist rant for another day, and confine my remarks to these: whatever grievance, whatever complaint, whatever legitimate issue any group has with the government and people of the United States, killing nearly 3000 of her citizens is not the way to see them redressed. It is an unabashed act of war, and should be met as such.

The first casualties died in an instant, or over a few hours. The most tragic death, that of our restraint and civility, has taken much longer.

This is a fight that we would rather not be part of, 9/11 notwithstanding. The enemy we fight will not rest until we are dead or under his thumb, our erudite and civilized conceits be damned, leaving us with no options but to engage and defeat them. With jihadis, this means killing them, destroying their assets, and making their side so sick to death of the fight that they abandon it. It means doing things that we want to believe we have outgrown.

Whether current policy addresses this or not is not my point; the dogs of war have not yet been let slip to the extent that they will be to settle this. We are fiddling, probing perhaps, maybe squandering global good will, and possibly making things worse.

But still I fear that the real fight is still yet to come, and at most, only one side will be standing at the end. Some day, not too far away, 9/11 will be dwarfed by the carnage that was first released on that day. Someday, soon, we will spit when some lawyer suggests our enemies should not be put to the knife or tortured or firebombed. Someday, soon, we will regain peace by means so horrible that a generation will not speak of it, like the the survivors of D-day kept silent as they came home to peace that they won by invading Europe, a euphemism for horrors best left at Normandy.

As much as 9/11, we also don't deserve this. Our creative spirit and enterprising energy will be turned from work and production to darkness and destruction. We will trample out the vintage from grapes of wrath. We will produce a General Sherman, we will leave a Hiroshima or Dresden smoldering somewhere in the middle east, we will napalm and clusterbomb and lay waste, we will become death, the destroyer of worlds. We look soft to our enemies, because we pursue things they consider decadent and immoral.

We are formidable, and dominate everything we turn our minds toward. We are energetic at making money, at working and playing and pursuing trivialities. How much better for our enemies if they had left us to that, rather than having us gird for war. The mujahadeen fancy us weak, and squeamish. They have yet to find out how misguided they are. We still care what the world thinks. We still have rules of engagement. When these conceits fall away, they will see what they have unleashed. Unfortunately, so will we.

You need not be a flag-flying patriot to see this coming, nor do you have to think that our country is always right. To a very real extent, once the existential threat is perceived, moral calculations will give way to something more grim.

Our enemies will appeal to our better instincts, and they will find none. They still walk because we are decent people. That will end, and they will rue the fact that they had many chances to stop the march to oblivion, just as we rue the fact that we did not stop 9/11 beforehand.

As I mourn the deaths of 3000, I mourn also the rebirth of the demons of war. If it be possible, let this cup pass us. If not, God help us all.

C'mon, Boy!

2006-09-11T19:44:00.000-04:00

There's no reason to read the title of this post with a Mickey Mouse falsetto, despite the fact that it is about Pluto. The planet. Or, these days, the dwarf planet Pluto.

Pluto has been reclassified as a dwarf planet by the International Astronomical Union for a variety of reasons. Scientifically, I don't think that it matters very much, but my prediction is that people will react quite negatively to the change, and looking at the status of the Wikipedia article, I think it's going to get ugly, stupid and petty. It feels like it is being demoted, in a way. And most everyone who has gotten past first grade has learned the canonical 9 planets with Pluto at the end, despite the fact that Pluto's orbit is sometimes inside that of Uranus. Nevertheless, the IAU realized that the discovery of objects in the Kuiper Belt and outside the plane of the ecliptic where all the other planets circle (well, ellipse, really) around the sun would lead to a muddle of planetoid objects unless the definition were tightened. And Pluto, while not making the cut as a planet for a handful of reasons, is now a dwarf planet.

This new category now includes Ceres. Ceres is the largest of the asteroids, though it is not made of the same stuff as the other asteroids and is probably independent of them in origin.Ceres looks a lot like a planet, seems to have some sort of atmosphere, and has weird surface features that are at least evocative of a planet. These aren't well understood. Still, being round makes it look enough like a planet that I'm glad that it falls into a category different from all of the other, potato-esque asteroids. It was even listed as a planet in the 1800s, along with a couple of other asteroids, Vesta and Pallas. Until the Pluto dust-up, I didn't know this. Vesta is the brightest asteroid, and usually the only asteroid visible from Earth except under unusually good conditions, though it is much less massive than Ceres, and very tater-shaped. So it doesn't make even the dwarf planet list.

Another dwarf planet that is particularly interesting is Xena, or as it is currently known, 2003 UB313. It orbits way outside the plane of the ecliptic, and is currently about as far away from the sun as it gets. Even so, it is visible with a modest amateur telescope. Xena is not the official name of the planet, but has caught the popular imagination. So much so that its moon is unofficially known as Gabrielle. Xena was one of the reasons for the crisis that lead to Pluto's reclassification, since it is actually larger than Pluto, and is the largest known dwarf planet. I won't place any bets as to whether the IAU will have the imagination to adopt these names, but my guess is they will stick in common usage, just like most of us will always think of Pluto as a planet, despite the astronomy nerds contention that it is a dwarf planet, dammit. Prosperpina (ugh!) and Persephone (not much better) has been suggested, and follows the IAU rules/traditions, but I'll always call it Xena if they pick something as constipated-sounding as that. Who made the IAU planet poohbahs anyway? I certainly didn't vote for them.

UPDATE: The IAU has chosen the name Eris for 2003 UB313. Eris is the name of the goddess of discord, and considering the discord Eris' discovery caused, the name fits. Oh, and Gabrielle? Eris' moon will be known as Dysnomia, the demon of (wait for it) Lawless-ness.

Very Superstitious

2006-09-05T22:55:00.000-04:00

An interesting article in the British TimesOnline suggests that humans evolved to be superstitious, because of the way we reason intuitively about mechanisms that are hidden from us. This fits in nicely with Boyer's Religion Explained which I have mentioned before, where it is argued that the human tendency to see agency behind natural phenomena explains the prevalence of gods in human culture.

It may be that, despite years of training in science, my mind is just such that I cannot, ultimately, throw off this intuition of an intelligent agent being behind things, as abstract and scientific as I have tried to make it (or It).

Or, perhaps we evolved to perceive the presence of the Almighty. My early fascination with Teilhard de Chardin may explain why I find this so compelling. Perhaps even more so are his delightful heresies concerning the Omega Point and Christogenesis, but this I will leave for another day.

Agnosticath

2006-08-29T21:29:00.000-04:00

No, an agnosticath isn't the fossil fish some fishermen found back in 1938- that was the Coelacanth. But some people have asked me to clarify my religious position, and Agnosticath is the best way I can figure out to describe it.

I have no problem describing myself as Christian, though I don't like calling myself 'a' Christian, though I will in the right context. Using the article implies something that I usually don't mean. I don't lend any special credence to a one-time born again experience that ushered me into the ranks of the 'saved', so I'm sure that even if I were a 100% dues-paid-up Roman Catholic, a lot of my evangelical friends would exclude me from the fold. And that's OK by me.

The person known as "Jesus" (an unfortunate Hellenization of something that probably was more like Yeshua) nevertheless occupies a fair amount of mental real estate for me, and because I move in circles that include both the washed-in-the-blood and the unrepentant heathen, with pretty much every grade in between, I have been quite happy to be both 'Catholic' and 'agnostic', with emphasis placed on who I wanted to argue with. Agnostic to the Catholics and Catholic to the Agnostics.

The question is, for most believers, and by default, for most non-believers is "Who do you say he (or He) is?"

I'll get to that. And to why it isn't really possible for me to just believe or not believe.

I picked the mosaic picture of Christ for a couple of reasons. First, I think that it is important to recognize that the picture that contemporary people have of Christ is, in fact, made up of many different shards. Looked at through mostly closed eyes (eyes closed to the history of Christianity, and of the multitudes of god/man myths) the picture appears continuous. As if it were not constructed, carefully, by many hands very conscious of wanting to control the image.

But that is very much an illusion. The 'Jesus' we are taught about as Sunday School children never existed(yes, I know most Catholics don't go to Sunday School. I was raised in a thoroughly heterodox environment, though). The sort of sleepy, dreamy Jesus who just loves everyone, who won't let anything bad happen, who never had to take a shit and knew from infancy everything that would ever happen just isn't there, now or in history. He is imaginary.

I'm not in the camp of those who think Jesus, the man, didn't have a physical existance, but boy, they are interesting, and worth a look. I'm just saying that whole story of Christianity isn't just what is written in the Gospels, because Christians were Christian before there was a written Gospel, and the writers of the Gospels had agendas, as did the people who decided which of these got to be the official stories.

Likewise it isn't possible to get the full image from Paul's epistles, because Paul might well have been trying to graft Jesus onto the "Sol Invictus" cults that he was familiar with. Retasking the existing myths and holidays was great sport back in the first few centuries of Christianity. (If you think that my contention that Christian tradition is a retooling of mainly sun worship mythos, consider that you go to Church on Sunday. This isn't coincidental. It was deliberate, back when Christianity had competition (until it killed off the competition...)) While this sort of unabashed syncretism is now considered heretical, to be heretical is necessary when founding a religion.

In the same vein, many pew-sitting Christians would be disturbed to realize that the Trinity is not mentioned in the scripture, that a council of human beings decided this (along with the divinity of Christ, which is only obliquely referenced in the Gospels, and only in later Gospels). They would like to believe that it was all handed to the Church as Jesus ascended into Heaven, in the Bible or Catechism or Book of Common Prayer. That it was handed to Man by God, written in the Elizabethan English that Jesus himself spoke.

The fact is that I don't know how much of the story is reliable history, and neither does anyone else, nor do I think that it matters, at least not to the value of the story. The contortions people go through to 'harmonize' the Gospels is a small indication of the pressure that they must feel to relieve the cognitive dissonance that having a set of stories that they feel obliged to believe, yet are demonstrably self-contradictory. It is, in the end, an admission- if they really thought that the Bible were inerrant, they'd just believe the contradiction. That they cannot suggests that they recognize non-contradiction as 'logically prior' to faith in the Bible- that they think that even God is bound by logic and non-contradiction. As one releases the Bible from historical constraints that are inappropriate for such a book, and as one is able to recognize allegory, this is less a problem.

The fear that sits at the heart of a need for biblical inerrancy is unwaranted I think, because it misses the point of religion and the Bible. There are Christians that recognize and celebrate the heterodoxy inherent in a movement as radical as early (pre-Constantine) Christianity, back whe it could still remain connected to the important part of Christianity, which is not belief, nor faith, but experience.

What experience do I mean? I mean this- the Christian understanding of the divine is that it is experienced in others, in other human beings. The making of God into Man is not to exalt humankind, nor to diminish God, but rather, to give the two a common vocabulary. The experience of the Resurrection is the experience of encountering undeserved suffering unto death, and yet, having the story continue. The Savior exits, but tells us that we can know Him by knowing ourselves in community, and in fact suggests that this is the only way we can know Him.

And the sin that pervades is lifted by faith- not belief, which is what is apportioned to the evidence, which as I have said, is scant- but to hope in unseen things, the hope that we can do what I see as the 'Christian Two-Step': see Jesus, be Jesus. We see Christ in others, and seek to serve. We be Christ for others, and relieve suffering and hunger and fear. The faith is that the experience is significant. That it is a sign of something deeper.

So, I have faith. Not in a book. Not, in the conventional sense, in God. Not in a person, but in a Person. One who lived 2000 years ago? How do I know? I encounter this Person in the people I meet, in the service I imperfectly try to render, in the struggle against the injustice I see. Do I believe in Jesus? What possibly could one mean by that? Who do I say He is? The Christ. Everything else, I don't know. Hence, Agnosticath. Irrational? Yeah, well, so's your old man.

Why a scientist talks all this faith/God stuff will not be apparent to some in the scientific camp, who are happy to embrace an unfettered athiesm. I recognize the drive toward intellectual purity that sits at the heart of this, an unwillingness to believe in something for which there is no evidence. That's why I made the distinction between faith and belief above. I have faith, in that my experience fits into a schema provided by Catholicism as I parse it, that leads me to try to love and serve others. I won't defend belief in the irrational. I fit the world into the schema without making demands on belief. I find it to lead me to be something that transcends what I would be in its absence, something that I find that I can live without, but still choose not to forgo.

To the persistant few, especially the "New Atheists", that want to purge the Earth of all religious belief- whence flows something so quixotic and irrational? Why do you demand that the rest of us bow to you, or suffer your denunciation and derision? Irrationality is human to the core, and how is one to look at your attempts to dictate what others think, other than to equate it with flinging feces like many other primates encountering a threat. Science, the intellectual love of my life, is the anomoly, and seeks for itself far more that it will ever have, and more than is warranted. Science as a process does not keep scientists from being irrational as hell. But good luck. It is an interesting and fun project to watch, and I support the confrontation of bigots and prigs and fools. It is a worthwhile endeavor, in parts. Doomed, but fun to watch.

Most of my Christian friends probably think I throw it all away because I won't say I believe in the Bible or Jesus or God or St. Prude the Incontinent or whomever they think is central. So be it. I won't bend to your demands, either.

There is a a bit of self-contradiction inherent in my position, and I recognize it. I It would be grand to just jettison it all. But it would be dishonest, and destructive to me, and I don't intend to back down. So, Agnosticath it is.

Skepchick

2006-08-29T20:30:00.000-04:00

One of the most interesting things about the internet is that there are fora for people with just about any interest. I find things like skeptical examination of paranormal, religious and pseudoscience fascinating. Much of the time, I just find myself nodding in agreement with what I find written. Occasionally, I find myself alarmed at what people will believe, or angry at how people prey on the poor critical thinking skills of others. And occasionally, I'll find something both delightful and challenging, like the forum at skepchick.org.

Skepchick is a forum for women about skeptical inquiry. To be blunt, it never occurred to me to think that women would have any particular take on the issues involved. I try to be egalitarian- not rascist or sexist, while not patting myself on the back for my 'enlightenment' and not overly nationalistic, while not adopting some overweening 'trans-nationalism' that I rarely find sincere. Nevertheless, as I read posts at skepchick, I find myself guilty of making assumptions along with male posters there, assumptions which are often exposed for what they are in short order. It is interesting to see this, because the shock of recognition of something in myself that I have tried to avoid reveals something interesting, something hidden from my view. It's a mystery being uncovered, in a way.

I have been married for 14 years, so I have had plenty of time to see how my wife's mind and my own are different, though I wouldn't overgeneralize it as exclusively gender- or sex-related. Both she and I take somewhat unorthodox approaches to things. In my case, it is both cause and effect with regard to my scientific career. Being a scientist makes you think about stuff in a somewhat hyperanalytical, instrospective way. These habits of mind, however, are probably necessesary for a person to want to be a scientist.

My wife fits the traditional female role well, yet she overflows its banks, to be as good a carpenter, or handyperson as most anyone I know. She's petite and pretty, yet (and I say this with no hint of irony) there are few men I would rather have at my back in a throwdown. (You'd have to know her. She can use a gun and a club with skill and without compunction. And we really are not that kind of people, honest. But it's nice to know we could be, in a pinch. Are my Kentucky roots showing?) I think I have seen much that would dissuade me from much sexism. But she always hands me the map when we travel. Even when she won't let me drive.

So, thus prepared, I still find myself going along with suggestions made by posters at Skepchick that women are more susceptible to, as one person put it, 'woo woo' psychic nonsense. Perhaps, it seems that there are cultural/gender dimensions to what kind of "Bullshit" one is inclined toward, but I think that it is pretty clear that everyone has inclinations to believe stupid crap that makes one more comfortable, or feel more powerful. The world is big and bewildering, and it isn't surprising that verbal primates (hey, that's us!) would use verbal means (myths, folktales, lies, you name it) to make sense of it.

Science Geek Heaven

2006-08-27T16:15:00.000-04:00

There are a lot of really cool resources available on the web. I've been fooling around with a package called Scilab. It's kind of like the commercial package Matlab, in that it will solve all sorts of equations, make graphs, and allow one to create systems to be simulated. It's free, too. I love the interweb.

Embryonic Stem Cells

2006-08-27T15:33:00.000-04:00

This is a subject that divides a lot of people. As potential human life, human embryos deserve our respect. They are not, I think, comparable to any other clot of tissue because of their potential.

Should embryonic stem cell research be allowed? I think that it is permissible if the life of the embryo is not compromised. With the consent of the parents involved, I do not see that taking some cells from an embryo in a fashion that would not kill the embryo as problematic.

However, this raises a lot of practical problems. What sort of experimentation would have to be done to prove that this could be done? Would this not require all sorts of potentially damaging things be done to embryonic life?

I think that there is a danger in being too cavalier. I do not consider a freshly fertilized human zygote to be the moral equivalent of my 8 month old. But I think that we need to approach the fertilized human egg with awe and respect; to do less would be to devalue the life that such gave us. There is enough contempt for life in the world without science participating.

One somewhat questionable approach is to say that one should only use embryos that are going to be discarded anyway. On one hand, you are rescuing knowledge that could potentially help desparate people. On the other, you are participating in the destruction of life. There is not a guarantee that anything useful would be gained, some say.

But it is guaranteed that much will be lost by discarding unused embryos. The life that we value, by resisting the use of stem cells from discarded embryos, is certainly harmed by willfully remaining ingnorant. There seems to me to be a very narrow road that one could travel, that would make sense scientifically and ethically.

Dubious Data

2005-12-23T14:47:00.000-05:00

Stats.org has their Dubious Data Awards up. Anyone interested in science in the media would do well to give it a look.

As a scientist, I deeply believe that scientific method is our best hope for solving the problems of mankind, as well as for exploiting opportunities to just make life better. I think a lot of laypeople feel this way, but there are also many who view science with suspicion. This, I think, is good, and frankly, a part of being an informed citizen is figuring out how good your information is. No one claiming expertise or authority to speak, however, deserves a pass. We need to look askance at journalism, too, which is (often unwittingly, but not always) complicit with hucksters and alarmists just as often as it is in cahoots with big business.

Most of the time, it just isn't possible for the average person (or a non-specialist outside his or her field) to evaluate the claims made in news reports about new medicine, or hidden dangers possibly lurking in our water supply or being beamed from our cell phones. Scientific sifting of information is far less likely to occur than exploitation of the info, however misbegotten, by people in politics or fundraising for special interests. Sites like Stats.org, with no particular political axe to grind, are a good resource. We need a set of basic scientific and statistical tools to know how seriously to take the reporting we read. I think I will devote a few posts to this soon.

An unexpected connection

2005-12-22T20:12:00.000-05:00

I have a friend at work, an electrical engineer. I'll call him Bob. Actually, I always call him Bob, because that's his name. Anyway, Bob is a really nice guy who will answer my ignorant questions about electronics with a smile, a diagram, and a patient explanation of what I should do.

I had need to measure a temperature, and had a nice sensor picked out to do it. However, I needed to amplify the signal. No big deal, I thought. I know a little electronics, and routinely build things to measure stuff. But I hit a thorny (to me) problem: if I amplified the signal so that the variation in temperature would produce a useful voltage change, the value of the voltage would be close to the highest voltage my analog to digital converter could read. Hmm, I thought. Time to talk to Bob.

The solution he showed me was to use an op amp and input a small voltage that would be subtracted from the output value. The variation in output caused by temperature change would be easily resolved by the A to D, and I had plenty of room for the temperature to swing up or down.

The solution is probably very obvious to an EE. I, however, am not an EE, but a chemist with enough electronic knowledge to do some things. Bob showed me how to solve my problem using the graphical shorthand common to electrical engineers, drawing the parts, and reasoning, aloud, in a logical but only vaguely mathematical way about what voltage would appear here or there, and he led me through the way the solution worked. I understand the shorthand well enough that his trick is now in my arsenal of cool electronic things I can do. I am sure he would have been happy to just draw me a circuit to solve my problem, but instead, he taught me how to solve an entire class of problems for myself.

Skipping to another conversation I was having with a technician in the lab: We needed to change a part of a molecule so that it would be more soluble in a particular solvent. To anyone who cares, we were going to perform a transesterification. I drew the molecule on a white board, using the graphical shorthand common to chemists, and led my friend through how the parts of the reactants formed and broke bonds, and how we got the product we wanted, in a logical yet only vaguely mathematical way. The principle thus illustrated, the technician has a new reaction in her arsenal of cool tricks to make new molecules. I could have just told her what to mix together, but now she knows a new synthetic technique in chemistry.

In both cases, Bob and I could break down the problem using a simplified diagram of the problem, one that hides all but the most essential features. In no way do they reflect the underlying reasons why the systems act the way they do. Yet it is possible to follow the rules for manipulating the diagrams, tempered by a few chemical or electrical engineering principles (very simple principles, in both cases) and come to useful solutions to problems.

The graphics and rules for their manipulation hide all the details. There is no indication of the physics or chemistry underneath. But the explanations are good enough so that someone skilled in their interpretation can do something useful based on them.

It hadn't occurred to me that the same general approach works for chemistry and electronics, though I work with both quite a bit.

My brain makes my wife angry

2005-12-03T17:12:00.000-05:00

Very interesting post in at LiveScience.com about how we tune some things out and pay attention selectively. Over the years I have had to do a lot of studying, and became pretty adept at focusing on what I needed to read and blocking out everything else. Being married, this ability takes on a certain double-edge, though...

Neuroscience is cool. It turned me into an agnostic, though. When I was in my early twenties, I was a Roman Catholic seminarian. I planned to be a Jesuit priest, so I could get a heapin' helpin' of both science and religion, since Jesuits are often trained in something "worldly" as well as being ordained.

Anyway, one afternoon, during Christmas break, I was home from seminary and in the local public library. I picked up a copy of From Neuron to Brain and began reading. Sometime in the course of reading the book, I realized that the only reason I still believed in God was that I couldn't see how consciousness could be explained without God. I just didn't know much about the problem, having only seen it from the philosophical side in school, where it appeared intractible to me. The instant I got it into my mind that consciousness would succumb to scientific scrutiny, my faith began to erode.

Now, the fact that it was held up by only this thread suggests that it had been in trouble for a while, and indeed it had. I had long gotten over my childhood belief that the Bible was an accurate account of anything, since I could read the official version and see that it was not internally consistent. (I truly wonder about the sanity of anyone who claims that the Bible is inerrant. I don't see how, since it states plainly in many places that two opposite things are true. QED. I would like to head off anyone who would engage in argument on this point by referring them to the Skeptic's Annotated Bible. They use the KJV, but bring your own along, just in case...)

In the course of my adolesence, when my love for science really took hold, I had rejected arguments from authority, or arguments from adverse consequences ('If you don't believe in God, you'll go to Hell!' isn't a reason to believe, it's a threat not credible to someone who doesn't already believe. It is also a favorite 'argument' of preachy types.) After threats and dubious holy books, the final reason to believe is to get along with the group, I guessed, and I had also rejected that as insufficient. But I couldn't account for the 'miraculous' fact that I was meat that had thoughts.

I won't prattle about deconversion and the emotional anguish it causes. There are a lot of good social effects of religion (whoa, atheists, I'm well aware there are plenty of bad ones, too) so I subscribe to a utilitarian view of encouraging whatever good comes out, and denouncing any bad. I don't get any fun out of poking holes in people's worldview (I like Pascal Boyer's Religion Explained, a evolutionary psychology of religion that makes me think that irrationality and religion are inevitable, so I'm not going to waste time fighting anything but the excesses I see. It would be as fruitless as prohibiting sex, I think).

In the past few years, I've been reading what I can of Daniel Dennet and Patricia Churchill. I'm not clearly convinced by Dennet's Consciousness Explained, but I think it may be because people are just not wired to understand the sort of explanation of minds that science can give, or may be able to give as we learn more. It does dispense with a lot of what we intuitively believe, but the result is pretty non-intuitive. Just like we found at the bottom of physics and chemistry with quantum mechanics, a real explanation of consciousness might prove incomprehensible, yet demonstrably accurate.

Richard Smalley, 1943-2005

2005-10-29T23:55:00.000-04:00

Richard Smalley shared the 1996 Nobel Prize in Chemistry with Robert Curl and Harold Kroto for the discovery of buckminsterfullerene, a molecule made from 60 carbon atoms. It was named after Buckmister Fuller, an American architect and inventor who designed the geodesic dome, a structure that looks like the fullerene molecule.

The discovery of buckyballs was significant for many reasons, but a few stand out. First, it represented a new allotrope of carbon (allotrope is a fancy word for the for structural forms an element can assume). Before this, only graphite and diamond were known allotropes. Since then, nanotubes have been discovered, as have higher fullerenes with many more carbon atoms. At the time, however, it wasn't known that elemental carbon could be so diverse.

Second, with the exquisite symmetry of the molecule, the properties were expected to be remarkable, and they are.

Finally, discovering that carbon could form into perfect little sphere-like molecules started people thinking seriously about nanotechnology.

Generally, the discovery of a single molecule gets little press. With the discovery of buckminsterfullerene, Professor Smalley was instrumental in the touching off of a fertile new area of scientific exploration.

Nanocars

2005-10-25T18:48:00.000-04:00

Jim Tour is one of my favorite scientists. He does a lot of impressive work in the area of molecular electronics and nanoscience, which was my research field as a grad student and post doc. Tour is hard-working as hell, and has a sort of showman's flair for promoting his work that only occasionally spirals off into the hype that the field is infamous for. Now, though, his group has announced a piece of work that is both significant and yet 100% showboat: the nanocar.

The car (pictured in the molecular model above, riding on a street made of gold atoms ) is put together out of fairly straightforward parts, at least from a synthetic chemist's point of view. However, the wheels are fullerene, the 60-atom molecular allotrope of carbon that Tour's colleague at Rice, Richard Smalley, shared a Nobel prize for discovering. Fullerenes are really cool molecules for lots of reasons, but they are a nightmare to modify synthetically. So putting the wheels on this bad boy was a bitch.

Once they got the thing together, they dragged it along a gold surface with the tip of an atomic force microscope, and they showed that it rolls easier along the direction the wheels roll than from side to side. This isn't surprising to anyone who has played with a toy truck; however, in the nano-realm, it is relatively easy to just slide things around on surfaces. The data Tour's group collected suggests that the wheels are really rolling, and the car is not just sliding.

I don't expect GM will be producing these anytime soon. However, people have been hyping nanotechnology for over a decade now, and there have been many pretty pictures made of nanomachines. But there has been precious little real molecular demonstration of all this promise. This work is goofy, yet compelling, and it isn't musing or theory. It's a molecule that you can put in a bottle, and it's all the proof anyone needs that nanotech, though still an infant, has a lot of cool discoveries in store.

Katrina

2005-09-11T22:04:00.000-04:00

There is an eclectic mix of people howling and pointing their pointy political fingers over the relief and rescue efforts following Katrina. (I will pretend, for the sake of concentrating my efforts somewhere other than dubious assignments of motives to other people, that everyone involved is yelling and pointing from concern with aiding the victims of the hurricane and preventing similar problems in the future.)

I suspect that screw-ups were occuring at every level, but I don't want to get distracted by the political storm that Katrina has spawned. What I am more interested in is studying the decisions that were made, and how they were implemented, or not. I don't want the truth as a bludgeon, but to see how to do things better next time. To find the failures, not to lynch the guilty, but to further protect people. So there really isn't much room for political shading of facts.

A lot of failure boils down to errors in judgement. Experience is highly valued, after all, because with lots of experience, presumably, comes ever better judgement. Only so much personal experience with once-in-a-century disasters is possible, so we also expect the experts to keep stewardship of the experience others have gained. To judge the relief efforts against such experience, we need the unvarnished data. We need frank assessment without regard to any existing political narrative.

Inevitably, natural disasters strike, and inevitablely, innocent people get hurt, and the people charged with helping them make mistakes. It sucks, it's unfair, and it always impacts most those least able to handle it. And when the dust settles, I am all for heads rolling, if the incompetence or malfeasance of those heads added to the horror and chaos.

But we are bound by decency to do our best to ameliorate the suffering now, forging ahead in fixing problems, even if we think the opposing political team is evil incarnate. I think the political debate would be served by knowing as much as possible about Katrina, the aftermath and the relief efforts. We should strive to learn from Katrina, and to prevent future suffering as much as possible, which means that the engineers and scientists involved need to put aside politics and look at the data and facts. Until then, the errors are just errors. It isn't entirely clear what actions were in error. When politics is involved, there are, as they say, 'competing narratives', so even basic facts need to be confirmed.

Katrina was a monster; not a record, but still a monster, and it hit a particularly impovershed and vulnerable part of the gulf coast. It will take a while, sorting through what went right and wrong, and figuring out how to use this information for something of greater significance than throttling political opponents. To do it right, we need to evaluate the response as objectively as we can. Using any untruth, however politically expedient, could potentially harm people in the future, and is no less an outrage than any harm done by the relief effort itself.

Please take a moment to donate to the relief organization of your choice; regardless of Katrina's final toll, which fortunately seems to have been overestimated, lots of people are displaced and suffering.

Devils from Mars!

2005-08-27T03:15:00.000-04:00

Dirt devils on Mars as photographed by the Mars Rover "Spirit". Space.com has all sorts of good stuff about the Rover Missions. It is generally filled with rich, geeky goodness, so check it out.

Not even my Mom reads this

2005-08-27T02:22:00.000-04:00

Science, to some extent, is the attempt to stop fooling yourself. I am a pro. My paycheck (such as it is) comes from doing science. Still, I constantly struggle with the tendency to jump to conclusions, or to discount data I don't already agree with. In the many years of training it took to become a scientist, I didn't learn a magical way to turn these instincts off. But I did learn to challenge my assumptions; I learned to require proof of myself. I developed skeptical habits.

My skeptical habits and analytical skills have made my life better. I would like to share what I can of them, and I sorta started this blog to give myself a chance to spread my gospel o' scientificity. And to share the cool shit that science uncovers in abundance. But...

Nobody reads my blog. Now, Dad stops by once in a while. My uncle has peeked in, but he may have lost interest, since I wait a while between posts. I'm not sure how many peeks I've had. But in the great bloggy scheme of things, I'm talking to myself.

So I will post to suit myself. I will devote the blog to science and skepticism, if only to clarify my own thinking. If someone reads it and is pursuaded, if only that I am a moron, well, hunky dory.

Oh, and I changed the blog name. Since no one reads this, I don't envision it being a problem.

Regional English

2005-08-13T05:04:00.000-04:00

Your Linguistic Profile:

45% General American English

20% Dixie

20% Upper Midwestern

10% Yankee

5% Midwestern

What Kind of American English Do You Speak?

Interesting mix. I guess the dixie comes from growing up in Kentucky. The upper Midwest, from living in Michigan perhaps. I don't know how this questionaire was put together, but it's fun. There are a bunch more blog quizzes at the site linked above.

Intelligent design

2005-08-04T14:40:00.000-04:00

I have read news reports that President Bush wants "Intelligent Design" taught along side evolution in public schools.

I'm against it because "Intelligent Design" is not science; it is a lawyerly turn of phrase, precison-engineered to legitimize the aim of asserting the faith of fundamentalists over science.

I don't plan to debate this here, because as it is I'd just be talking to myself, but I will state my position:

I think evolutionary explainations for the diversity of life on earth are far preferable to weak "God did it" arguments. They require real observations of real organisms, and produce data. Data can be flawed, and must be handled with skepticism and care. But with data and scientific method, one can correct mistakes, which one cannot with slavish devotion to the literal reading of ancient and venerable books, regardless of evidence.

Consider: I personally believe God did do it, indirectly, by imbuing nature at the outset with further self-creating potential. I recognize the attraction of Intelligent Design. The God I envision is the Enlightenment God, dispassionate, the architect of creation, whose cause is completely set into motion by some mysterious creative act, but then proceeds logically and, quantum mechanics allowed for, predictably. I have no scientific basis for this, but it is my intuition, questionable and dubious, but in the absence of an 'ultimate theory', what I will live with. A lot of religious people I love and respect would be unsatisfied with the God I posit, and a lot of scientific people I love and respect think I'm a goof for postulating any God. (Discussing it here makes me queasy, but I feel obliged to accurately represent what I think.)

This sort of idea of God would not sit well with ID proponents, I imagine. I'm unaffiliated with orthodoxy of any sort, and I don't hold any book, congregation or council, however revered as holy, as counter to scientific data, where it exists or could exist.

So why am I not a "Deist for ID" or the like?

I sometimes believe things without evidence, of course, but I try not to assert stuff without evidence. I might discuss that I think God, as I conceive God, created the universe, but past what we can measure, I do not expect anyone else to care.

I think evolution is natural and undirected.

I respect the uninformed who are skeptical about evolution, but I have no time for people who knowingly distort things to make a case. Liars for God are still liars.

I think science must proceed as if the universe is intelligible to do science. It seems logical that whether God exists or not, the universe still could be unpredictable and/or unintelligible. But we are constrained to look for order, and explanation, if science is to yield useful knowledge.

What people believe about God is not my concern. It neither picks my pocket, nor breaks my leg, to borrow from Thomas Jefferson. I think that mixing religious faith with science will do great harm to both, though.

Ayn Rand

2005-06-05T03:10:00.000-04:00

I've read a few of her books. I'm not so sure she was the bastion of rationality she claimed, but I do think that the individual should be favored over the collective, if only because I don't want the collective telling me what to do. On the other hand, I don't want Ayn Rand telling me what to do either.

Really, though, I am just farting around with HTML code, and wanted to try this out. I don't know diddly about web programming, but I am starting to fiddle around. I program in C++ or LabView when I have some project I need to do. I do a little C programming for embedded controlers. But there are a lot of cool things one can do with web pages. I am especially interested in Java script, which will let you do all kinds of stuff. But I find it difficult, as yet, to get things to work.

Will phthalates shrivel your nuggets?

2005-06-01T22:23:00.000-04:00

New Scientist has a story with the shocking headline " 'Gender-bending' chemicals found to 'feminise' boys ". In it, the implication is made that a new study shows that chemicals called phthalates are harmful to the sexual development of infant boys. In contrast to the sensational headline, the article body uses words that are slightly more weasely: it says the results "suggest" adverse effects of phthalates on genital development in baby boys. This sounds serious. Let's look at it.

Phthalates are common plasticizers used in cosmetics, plastics, food containers (including pop bottles), infant toys etc. This is a chemical to which people have been and are routinely being exposed . Despite years of concerns being raised, though, these substances have never been shown to be a hazard.

So, do phthalates shrink testicles, or more accurately, cause genital defects? Well, if they do, you can't tell it from the study to which the New Scientist article refers. Stats.org at George Mason University points out that the study did not even consider this hypothesis.

Are phthalates "gender bending" like the headline says? High doses cause problems in rats, known as incomplete virilization. In extreme cases, the genitalia can be ambiguous, not clearly male or female. So far as I know, no data exists for humans at high exposures. Phthalates haven't been shown to have effects in human until this study, says the New Scientist article. So even if this study could be counted as evidence for this, which it can not, it's only one study.

I'm not an expert in this field, but I can apply some general scientific knowledge to evaluate the article . If the study didn't test a hypothesis, then it isn't appropriate to interpret it as lending evidence to that hypothesis. So if the study shows anything at all, it is not showing that phthalates affect genital genital development in humans. This wasn't even considered.

And if you read the Stats.org description of the study results and their statistical significance, you'll see that there was only weak correlation between the phthalate metabolite concentration in mother's urine and the calculated anogenital index, a ratio defined by the distance between the anus and the base of the penis divided by the weight of the child at the time of measurement. Other ratios, like the anoscrotal index, didn't show a correlation. Whatever the study did show, it showed poorly. So poorly that no conclusion can be drawn; none of the phthalate/ anogenital index correlations passed the test for statistical significance. One can't conclude that any of the phthalates had any significant effect based on the meaurements made. The study results don't suggest that phthalates cause genital problems or otherwise feminize boys, and it is incorrect and misleading to suggest otherwise.

I am completely sympathetic with anyone who wants to avoid exposure to chemicals, and understand why they would want to protect their children from them. The term "chemical" is intimidating, especially in light of what the term can mean. "Chemical" can mean things that are corrosive, caustic, foul-smelling and toxic. Some things chemical are clearly dangerous. Some are dangerous while looking benign. And some, a good many useful things, are innocuous when they seem threatening. We really only know by doing the science. We should not ignore data that shows that something is harmful, but we also need to recognize when the data says we have something that is useful and not harmful. It isn't helpful to trumpet non-results in a frightening and confusing manner. It is deceitful to conflate detecting something, and that something being automatically dangerous or even significant.

Is it useful to continue studying phthalate saftety? I think that it is possible that someone might have a genetic predisposition to sensitivity to phthalates, and I would like to see this studied. I don't know of a way that one could prove unequivocally that a substance is not harmful to anyone under every reasonable set of conditions. But I think that lack of proof of harm, in spite of vigorous efforts to find it by people completely free of chemical industry influence, means we can go on using things containing phthalates without fear.

Global Warming Catfights

2005-05-29T02:51:00.000-04:00

The global warming debate is fascinating. Even referring to it as a 'debate' is enough to raise hackles on the side of the faithful, certain that nothing short of rolling back the industrial revolution will save the planet.

Climate is very complex (!) and computer models of it are far from certain. I am not going to wade in here; I have my opinions, but the field is so complicated, and I am so unexpert, that I wouldn't add anything except bloviation, and there's all that anyone needs all over the internet.

For an interesting look into the kind of fights underway, I would direct you to two sites, Climate2003.com and Realclimate.org for insights into one little section of the debate. The Climate2003 site has been supplanted by climateaudit.org.

One thing to watch for in the posts and comments of the sites are evidences of very unscientific attitudes, like denunciations, ad hominem attacks, obfuscations, and reluctance to share information, like data and methods, this last fault lying largely on the pro-global warming side. The whole thing stinks to high heaven, in my opinion. I am skeptical by nature (comes with the scientific territory) but I will generally bow to the experts when I have no good reason to doubt them. These guys are giving me lots of reasons. They might be right and righteous, but it stinks.

On the other hand, even if their data, models or methods suck, it doesn't mean that global warming isn't occurring, or that humans aren't playing a part, even the biggest part. It just means that they didn't prove it. .

I can comment on the debate without wading into the scientific waters, which I have admitted are over my head. What bothers me most is the constant harping on the "consensus" of climate scientists regarding global warming. I think that it isn't clear that there is a consensus, but, damn it all, if science has any lesson, it's that consensus can be wrong, and heresy has to be tolerated. Until 1905, scientific consensus was that Newton was right. Einstein took care of that, and then some. And any scientist who isn't up to a full frontal assault on his ideas ought to consider another line of work. Anyone who rejects a criticism of scientific canon is being unscientific unless some basic principle, like conservation of energy, is being violated. Climate science is impressive, but it isn't at the point of being natural law.

The faithful will claim that the negative consequences of global warming are so dire, we can't wait for the science to be certain. This sort of argument is fallacious. It's like someone saying that you have to believe in Cthulu, because if you don't, he'll send you to the netherworld. Not if he doesn't exist...

Calculations

2005-05-29T02:05:00.000-04:00

I do a lot of calculations in my job. I use Microsoft Excel, MatLab, and Igor to analyze data. To gather the data I use LabView. This sort of thing is something I'm used to associating with being a scientist or engineer. I had never really thought much about it outside this arena, though.

Recently, I found a really neat site recently called Political Calculations, billed as "interactive tools for interactive politics." It's full of interesting data and lots of interactive web apps to calculate interesting stuff. One post I particularly like is one about deciding whether medical tests are worth the costs, based on the cost, the likelihood of doing any good, and how long you are likely to be around to enjoy the benefit.

It's come as a revelation to me just how interesting the work of economists and political scientists can be, especially those with a quantitative bent. Following some of these, I have found some cool data online. I am no economist, but I can follow the data provided at the Bureau of Labor Statistics site well enough to make my points when arguing with my friends about the likely effects of raising minimum wages, for example.

As a physics and chemistry undergrad, I had a pretty condescending attitude toward the social sciences. These days, I realize that being able to measure something to 15 decimal places doesn't make it relevant to society at large. I still think that there is a lot of crap that gets too much play in these fields, but it is clear to me that this is well understood in the fields themselves. There's also a lot of just really neat stuff being done, not all of it quantitative. If I could do it all over again, I'd be torn between being an economist and a physical scientist. Even more so if economics involved explosions and fires.

Crazy...

2005-05-27T15:23:00.000-04:00

Things have been a bit crazy, so I haven't posted in a while, but I haven't been idle. I'll be back very soon, with a few new things to say.

One hundred parts per billion

2005-03-01T04:06:00.000-05:00

Let's try to make the quantity 100 ppb concrete.

Assume you have one grain of salt, a little cube about 3/10 of a millimeter long (I'm estimating, but this whole exercise is about estimation). If that is so, we have a cube of 0.03 centimeters on a side, with a volume of (0.03cm)^3= 0.000027 cubic centimeters. The density of salt is 2.165 grams per cubic centimeter, so a grain of salt is about 0.0000585 grams (almost 60 micrograms).

Now, to get a solution that is 100 parts per billion by weight salt, we need to understand what is meant by parts per billion. Percent, which is more familiar, is basically parts per hundred. If I want a 10% solution, I want a 10 parts per hundred solution.

So lets do it for 100 ppb. To get 1 part per billion, I need a billion times more mass of liquid than salt, less the mass of the salt, which will be neglible, so let's ignore it. So 0.0000585 grams x 1,000,000,000= 58,500 grams of water. 100 ppb is 100 times more concentrated than 1 ppb, so we can divide the mass of solvent by 100 to get 585 grams of water. One gram of water is 1 milliliter, and 500mL is about a pint, so we are talking about dissolving a grain of salt or two in a bit over a pint of water to get a salt concentration of 100 ppb.

Applying this to earlier posts, this is about the concentration of perchlorates being discussed. With respect to the methylmercury post, this is 1000 times bigger. The projected reduction in methylmercury content in seafood would be akin to one-onethousandth of a grain of salt in a pint of water.

Perchlorates as Medicine?

2005-02-28T21:07:00.000-05:00

Back in the 1950's, perchlorate was approved by the FDA as a treatment for hyperthyroidism. It appears that the dose is sometimes more than a gram a day. There does seem to be some worry about causing goiter in unborn children, whose thyroid glands are more susceptible to perchorate.

As I mentioned in the post for methylmercury, the dose makes the poison. It appears (from the review by Wolff linked above) that perchlorate passes quickly through the body, unchanged. This suggests that low levels in water would not be a problem for adults, because the dose is low, and the perchlorate isn't retained (except, perhaps, in breast milk as noted below). The toxicity reported in Wolff's review for adults comes only at high, prolonged doses and the harm caused to children in utero (caused by perchlorate crossing the placenta, after the mother ingested a gram of the stuff) is based on pretty high doses, certainly more than from drinking water containing perchlorate in the 50-100 parts per billion range. So I think it is likely that adults are not directly threatened by perchlorates in the environment (nor did the reports in the news suggest that there is any threat to adults. I'm just walking myself throught this, confirming that I come to the same conclusions). The original article that I linked about perchlorates suggests that breastfed infants would get too much, based on the levels in human breast milk. If the ion doesn't concentrate in the body, then the perchlorates in the water couldn't be the only source in breast milk. (I reach a conclusion from the article. I'm both fact-checking the article, and making sure I understand the issues involved.) So, where's the rest coming from? Irrigation water? Natural sources? Is it possible that perchlorate does get stored in some people? More to find out...

New books

2005-02-27T17:11:00.000-05:00

I recently downloaded a copy of Daniel J. Jacob's Introduction to Atmospheric Chemistry from his website. I intend to learn more about environmental science because I think that environmental debates are very important. Currently, I am far from convinced that the sky is falling. I am generally skeptical of the climatologists' ability to forecast future temperatures, but I agree that if global warming is occurring, and whether the cause is mankind, then we have a lot of work to do. Not necessarily to stop or reverse it (even supporters of Kyoto acknowledge that it alone could do little to change things, even if it is correct in its assumptions, while already being fantastically expensive) but to figure out how to live with it.

All this said, I admit readily that I am not an environmental scientist, and I have a lot to learn to fairly evaluate either side of global warming/environmentalism arguments. If I can make some sense of the pdf of Jacob's book, I'll pay the sixty bucks to get the hardcover from Amazon.

I also just received Classical Dynamics: a contemporary approach by Jose and Saletan. Nothing that's politically explosive here, like global warming, yet surprisingly, this area of physics has been influential in popular culture in the past couple of decades. Classical Dynamics, more often called Classical Mechanics, is a foundational subject in physics, and it deals with the motions of average-sized things. It's called classical to distinguish it from quantum mechanics, an altogether different kettle of fish concerned with very small things.

I had a course in mechanics when I was a physics undergrad, and have followed the emergence of new science from this oldest of physical theories since the 1980's. Chaos, fractals and complexity, which is where mechanics has begun to make a cultural impact, have emerged fairly recently. I was also a mathematics minor in college, so the inclusion in this volume of more modern mathematical techniques makes me excited to slog through it. Even when it's interesting, I find theoretical physics a hard row to hoe. Perhaps impatience is the best explanation for why I became a chemist rather than a physicist...

Glaciers and Volcanos on Mars

2005-02-27T13:07:00.000-05:00

The European Space Agency has some great pictures of the North Pole of Mars, taken by the Mars Express probe. It appears that there may be some active volcanos on Mars.

I am philosophically supportive of manned space exploration, but this sort of result, like those of NASA's Mars Exploration Program rovers Spirit and Opportunity, makes the case for doing as much as possible by robots before risking the lives of humans.

Then, there's the spectacular success of the Cassini-Huygens mission to Titan, a place we are not likely to ever send people.

There are people of all political stripes that think that this sort of thing is a waste of money. I disagree, and would argue that it stretches both our technical abilities and our conceptions of ourselves to explore in this way. If I have a complaint, it's that these results, and what they imply, aren't getting more media attention.

Benefits have costs...

2005-02-25T13:28:00.000-05:00

At TechCentralStation, Sandy Szwarc has an article on methylmercury in fish. Methylmercury is very toxic- but as with any toxin, the dose determines the effect. Szwarc points out that proposed emission standards might reduce methylmercury levels in seafood by as little as one-tenth of a part per billion.

There is some reason to question whether current levels of methylmercury in fish are dangerous to people or children in utero (for examples, follow the links in Szwarc's article). I'm willing to grant that if my wife were pregnant, I would suggest she eat fish that has the lowest levels of methylmercury. In the presence of perfectly good alternatives, chosing lower methylmercury fish is pretty much cost free.

However, if it is true that enacting new expensive mercury emission standards will reduce methylmercury in fish (and elsewhere in the environment) by so little, then the expected benefits don't justify the costs. Emotionally it can seem that any reduction is a good thing. But paying for something one place means that there isn't money for something else, so we should be circumspect about paying too much for too little benefit.