In the fall of 1984, at the start of my second year, I got to be the T.A. for Plant Taxonomy, a subject that I loved far more than first year biology. The class was usually taught by Fred G., but he was on sabbatical that year, so Jack was filling in, giving the lectures and overseeing the labs, making it all the more fun. Jack and I would walk around the campus with big, black trash bags, collecting plants for upcoming labs. Each lab featured a few plant families, represented by as many genera and species as we could find for that family. This gave the students a chance to see the themes for each family, the characteristics shared by all of the genera and species grouped within it. Most people can recognize many plants that are members of the grass family, but it takes a little more practice to identify a flower with parts in fours (four petals, four sepals, etc.) and an inferior ovary, where the seed-containing fruit ripens underneath all the other flower parts, as a likely member of the evening-primrose family. In a lab full of different grasses, or a jar filled with fireweed next to a jar of clarkia next to a bottle of willow-herb, students could more easily get a feel for the "themes" of each plant family, as well as variations on the themes, as expressed by the different genera and species.

The text we used was Flora of the Pacific Northwest by Hitchcock and Cronquist (1973), a book full of descriptions and technical keys used to identify plants. The book was distilled down in 1973, from a much larger five-volume set produced by Hitchcock and his colleagues in the late 1950s and 60s. Back in those days, you could get some real mileage out of a National Science Foundation grant without having to beg for corporate funding every year or so. The Flora was guaranteed to terrify many students, but I told them they were lucky - their flora was filled with beautiful line drawings reproduced from the earlier, bigger Vascular Plants of the Pacific Northwest. Hitchcock and his colleagues had managed to hire scientific illustrators for a number of years to produce the lovely and helpful drawings. The reference we used at UC Davis at the time, Munz's A California Flora and Supplement, was a huge single volume with tissue-thin pages. It contained only a few drawings to introduce each family; we keyed plants entirely from the technical descriptions, without any reassuring artwork. In addition to learning new plant families, each lab started with a quiz where students had to identify an unknown plant using the keys in the flora. Besides the lecture and lab exams, and the keying quizzes, each student was assigned a plant press and had to collect, press, identify and properly label representatives from 30 different plant families.

Mishtu B. was a fourth year forestry major when he took Jack's taxonomy class. During the first lab, Jack and the T.A.s talked about basic plant parts (you can't key a plant if you don't know what you're looking at), explained the keying quizzes and lab exams, and checked out plant presses to the students. To our surprise, Mishtu showed up to the lab with his own plant press, already full of specimens. Mishtu had spent part of the summer at forestry camp, required for the completion of his degree. Since he had planned to take taxonomy in the fall anyway, he figured he would get a jump-start on the plant collection, so he took his own press along. This was highly unusual, but he had managed to find some fine specimens, including some flowering stems of coralroot (Corallorhiza), a wonderful little saprophytic orchid - it obtains nutrients from the decomposing vegetation on the forest floor and has no chlorophyll, probably with the help of other organisms, such as fungi. Some of his field notes were entertaining to read, but the details were occasionally rather vague. Mishtu never had much of a sense of direction and, being a night owl, he often fell asleep in the woods during the day and wasn't always sure where he was. The label that accompanies each plant in a proper collection is supposed to specify exactly where it was found, but Jack noticed that one specimen had been collected from "deepest, darkest B.C."

Mishtu's father was a plant physiologist and his parents had immigrated to Canada from India, a place that has produced some very fine botanists. Mishtu was both shy and bold. He was addicted to caffeine, loved conifers, and had an innate understanding of things mathematical. He also enjoyed writing poems, including a tribute to the little coralroot he found:

"Corallorhiza, oh this beauty

Arises from young death like duty"

Mishtu started hanging out in Jack's office more often. He was interested in Jack's exploratory approach to the study of plant variation, and also intrigued by some of the theoretical discussions that were taking place. He later decided to pursue a Master's degree in Botany, with Jack as his supervisor, studying Alaska yellow cedar, called Chamaecyparis nootkatensis at the time.

Jack made a habit of sitting in on one particular class each Monday, Wednesday and Friday morning: Zoology 400, The History and Philosophy of Biology, taught by Cy Finnegan, an embryologist by training and the Dean of Science at the time. Some of the botany and zoology graduate students took to sitting in as well, along with Dan B., a young professor, parasitologist and systematist with an interest in some unconventional ideas about evolution. Several of us freeloaders of Finnegan's lectures, the "peanut gallery" as we called ourselves, would show up and occupy most of the desks in the back of the classroom. Though he never was much of a morning person and always came to class clinging sleepily to his coffee cup, Mishtu joined us as well, taking Zoo 400 for credit at one point, and sitting in later for fun.

Cy touched on many concepts, from Aristotle's ideas about cause and purpose, to the "paradigm shifts" described by Thomas Kuhn in his popular Structure of Scientific Revolution. I think Kuhn was overly optimistic - entrenched ideas often stay that was for long periods, even when they fail to expand any understanding of nature. All these years later, I'm still waiting for a revolution focused on evolutionary theory to take hold. Cy spent several lectures exploring Michael Polanyi's ideas about tacit knowledge and Carl Hempel's Covering Law Model. The course spanned the entire school year, so there was time to touch on a variety of philosophers, including some with backgrounds in biology. I was attracted by the theme that the sciences, including a science like biology, so messy in its complexity, must be intelligible and rational, even when it's not easy. Many famous biologists, such as Ernst Mayr and G.L. Stebbins, had argued that biology was too complex and had too many "exceptions" to follow the usual rules. But this "exceptionalism" did nothing for biology except make it weak and opaque as a science. How could we approach hypotheses and theories in biology in such a way as to make them as explicit and transparent as possible? How do we test them? What would it take for biology to be a "strong" science like chemistry or physics? Biologists have sometimes been accused of having "physics envy" because some of us would like biology to be as scientifically rigorous as physics tends to be. Scientific rigor should be of interest to all of us, and avoiding it must not be excused. I can't imagine being jealous of any physicist because biology, especially botany, is so much more interesting (and the job market in physics isn't very good either). What's different about many physicists is that they seem to be able to look at the universe in different ways without causing a great uproar among other physicists. They honor Isaac Newton, but they are not forced to pay constant homage to him. Since the days of Newton physicists have been wrestling their way through the ideas of gravity, followed by relativity, quantum mechanics, string theory, and so on. We biologists, on the other hand, are expected to incessantly praise and give thanks to Darwin. If we try to look beyond his (although it wasn't his alone) idea of natural selection, we are committing some sort of sacrilege. This is a tiresome practice that prevents us from asking serious questions about the prevailing theory, and about alternative evolutionary theories.

Cy Finnegan, of proud Irish heritage, was rather tall and thin, a World War II veteran of the Lido and Burma Roads. He had a New England accent he never did manage to lose in spite of many years in western Canada. He considered the job of Dean of Sciences to be a serious one and sometimes came to the morning Zoo 400 lecture looking as if he'd had a long night with little sleep. During our travels through the history of ideas about science, and what a scientific approach to the understanding of living things should perhaps look like, Cy Finnegan was always the guide, but never the judge. Students would sometimes try to get him to give an opinion about an idea or a philosopher, but they were always frustrated when he insisted it was their interpretation that was important. He was not interested in having own opinion repeated back to him.

"How long should the essay be?" a student would ask.

"As long as it takes you to make your argument," he would answer.

As one of the several student freeloaders, I never submitted any essays, but I was enthralled by the lectures and took copious notes (which I still have to this day, along with many of Cy's original notes - they form much of the soul of this book). I wish all science students or maybe all students in general) had the advantage of such a course, but the practical ( and impractical) importance of a passing familiarity with the philosophers of science may be too subtle for believers in the shallow business school model of higher education. First, we need to stop thinking that it's all about the patents and the money - it's not. Administrators (and coaches) are not a separate, higher life form than the faculty, staff and students, but they are too numerous and often overpaid. We must stop thinking that everything should be "run like a business," whatever that means - it shouldn't. Colleges and universities, among many other institutions, are not businesses and can't properly function as such.

Many people believe they have an understanding of the "scientific method," but over the years I have become pretty skeptical about this. It's not uncommon to hear ideas from science, especially ideas about evolution, accused of being "just theories," as if this were some sort of criticism. All science, even those assertions with the strongest empirical support, is theoretical. No serious comparison of ideas about evolution can be made without any comprehension of the strengths and limitations of science. Based especially on Cy's distillation of many books on (primarily western) science and its history, in addition to my relatively small amounts of reading, I think there are some important central themes.

Sometimes an example or a story is the best way to make a general point. Early on in Zoo 400, Cy re-told a story from the past that is both horrific and hard to imagine in the present.But that's what makes it a memorable example, something students may remember, even if other memories have faded. One of the philosophers Cy spent some time discussing was Carl Hempel and his Covering Law Model, a formal approach to generating and testing theories and hypotheses. In the second chapter of his book, Philosophy of Natural Science (1966), Hempel tells the story of the physician Ignaz Semmelweis and his work in the Vienna General Hospital. Cy repeated the awful tale about evidence, about observation, deductive reasoning, rejecting or accepting specific hypotheses as possible explanations, and the inductive moment of "Aha!"

During the years of 1844 to 1848, Semmelweis struggled with the grim problem of women dying shortly after delivering their babies from a nasty disease known as childbed or puerperal fever. The strangest thing was that the women were dying at very different rates in two maternity wards at the same hospital. He started tracking the deaths due to childbed fever of women giving birth in the First Maternity Division of the Vienna General Hospital, and found a mortality rate of 8.2% in 1844, 6.8% in 1845 and 11.4% in 1846. By comparison, the number of deaths from childbed fever in the Second Maternity Division, which was also part of the Vienna General Hospital, was much lower for the same years; 2.3, 2.0 and 2.7%, respectively.

What could explain this discrepancy? Semmelweis considered a long series of possible answers, testing and then rejecting each one. Was there a general epidemic of childbed fever in Vienna? No, the occurrence was quite low in the city and its surroundings - the "epidemic" seemed to be confined to the First Maternity Division. Women who went into labor and had their babies in the street, before reaching the hospital, had lower mortality rates than women giving birth in the First Maternity Division. Was it overcrowding? No, the Second Maternity Division was more crowded than the First Division, as pregnant women knew of the First Division's reputation and made every effort to avoid it. The food and general care of patients was the same between the two Divisions. The methods used by the medical students in the First Division to examine women in labor were the same methods used by the midwives in the Second Division, so student roughness was ruled out. What was different about the First Division? A priest giving last rites to a dying woman had to pass through several wards in the First Division, preceded by an attendant ringing a bell, but the priest could visit the dying in the Second Division without passing by other patients. Maybe that was it - depression and fear at the sight of the priest. Semmelweis had the priest dispense with the bell-ringer and approach the First Division by an alternate route. No change in death rates was observed. Semmelweis was becoming desperate. He even tried having the women deliver their babies in a different position. Nothing.

Finally, in 1847, an accident gave him the critical clue. A colleague of his was conducting an autopsy with a student, when the student slipped and cut his professor's finger with a scalpel. The poor professor died after exhibiting just the same symptoms as the women who had died of childbed fever. At this time, nobody knew much about sources of infection such as bacteria, but Semmelweis realized that the decomposing tissue from the corpse had gained entry into his colleague's bloodstream from the scalpel wound, possibly leading to illness and death from something that looked exactly like childbed fever. As it turned out, the physicians and medical students would often dissect a corpse and then go directly into the First Division to deliver babies after barely washing their hands. (Gross! This seems so obvious to us, but it wasn't in those days.) In the Second Division, with the low death rate, babies were delivered by midwives who did not engage in the study of anatomy through the dissection of cadavers. After forming and then rejecting the previous series of hypotheses, Semmelweis came up with yet another test. Instead of just a quick hand-rinsing, he had all of the medical students wash their hands in a chlorinated lime solution before touching patients. The mortality rate quickly began to drop, and by 1848 the First Division had a rate of 1.27% while the Second Division had a rate of 1.33%. The women who went into labor and gave birth in the street, before reaching the hospital, were generally not examined. They had escaped contamination, and this explained their lower mortality from childbed fever. Semmelweis later discovered that diseased tissue from a living person could also cause a deadly infection if introduced into the bloodstream of another.

The story of Semmelweis provides some grim examples of hypothesis generation and testing. It also reminds us that new discoveries sometimes come slowly - it took him a few years to test and then reject several possible causes of childbed fever. Though the wounding and subsequent death of his colleague was accidental, Semmelweis was paying attention when it happened, and it led to a hypothesis that could not be refuted. It was 1848 and Charles Darwin's On the Origin of Species would be published in 11 years. I'm willing to give Darwin his due for expanding the discussion of evolution (even if I think natural selection was and is an unsatisfactory idea). On the other hand, ideas about evolution had been knocking around at least since the 1790s and the days of Lamarck. It seems stranger still that some would like to give Darwin credit for ideas that wouldn't really be around for another 100 years or so. Relativity theory, complexity and who knows what else - Darwin thought of it all, we're sometimes told, in a Victorian sort of way. Darwin deification is still popular in academia, even though Alfred Russel Wallace came up with pretty much the same theory of natural selection at nearly the same time, apparently during a feverish dream. Many scientists of the mid-19th century were brilliant, certainly, but it was long ago and we were still figuring out that it's a good idea for physicians to wash their hands. Nowdays, often at the insistence of patients, they are overdosing with antibiotics instead, while knowing this encourages more ferocious strains of bacteria.

Cy Finnegan used Hempel's example of Semmelweis to introduce the general ideas of hypothesis formation and testing before getting into the details. Semmelweis gathered empirical evidence through observation and comparison of the two Maternity Divisions in an attempt to discover what differences about the First Division might lead to higher rates of childbed fever. He also engaged in a subset of observation - experimentation. He set up an experiment to see if the presence of a priest and his assistant bell-ringer had any real effect on mortality. He thought he might have discovered the source of the lethal fever when he observed the death of his colleague, and so he devised his hand-washing experiment to test whether preventing the transfer of decomposing tissue to the bloodstream of a healthy person would stop the disease.

Hempel ends the recounting of the Semmelweis story at this point, with the triumph of his discovery. You would think that the guy would have been honored, but he wasn't untiil later. Perhaps he became so obsessed with his new understanding of hygiene that he got in everyone's face until his colleagues couldn't take any more of him, maybe feeling that he was accusing them of being dirty or incompetent. Apparently, he was invited to tour a newly-built asylum, where he was lured inside, abducted and beaten. He later died from his injuries. So much for the appreciation of new ideas.