Saturday, September 30, 2006

Predicting the future

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

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.

Sunday, September 24, 2006

Assuming Facts Not in Evidence

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.

Friday, September 15, 2006

Dead Ends

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).

Thursday, September 14, 2006

Expert Opinion

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’.

Wednesday, September 13, 2006


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.

Monday, September 11, 2006


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!

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.

Tuesday, September 05, 2006

Very Superstitious

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.