Christmas and the laboratory

I like Christmas on Wednesday, because the 'natural' last day of work is ambiguous. The last days before Christmas are like a coastline, where we stop and stare across empty space at the horizon, taking stock of what can safely be left behind and what we need to carry into the new year. December is filled with parties; institutional parties, directors' parties, departmental parties, lab parties, parties in the labs of collaborators, home parties, restaurant parties. Optimistic grad students hang plastic mistletoe over laboratory doors, which are decorated with Petri dishes, bubble wrap, tubing, wires, glassware, styrofoam peanuts, disposable plastics, arranged into Christmas trees, snowmen, candy canes, reindeers or sleighs. Who should get a present? The boss, the supervisor, the alpha colleague? The students, the technicians, that lady who looks after the accounts, the guys in the storeroom, the person who sorts the mail? The IT guys who rescue you every time something interferes with your destiny of spending eight hours a day staring at a monitor, the janitorial staff who mop the halls every night, the people who run the cafeteria? Will there be an institutional Christmas card? Must we pay the postage ourselves? It's a business expense, right? Students catch the bus or the train or a plane or drive their cars held together with duct tape onto icy roads and visit their families and old friends who don't quite understand this mysterious world called the laboratory. 

We want to spend December cleaning up the lab and sorting out messes but it never happens. Everyone tries to clear their desks by finishing what needs to be finished. And then they send it to someone else who is trying to clean off their own desk. Most years, there a few hours on my own before going home, trying to decide what can be rescued from neglect, what needs to be written down so that I will remember it when the break is over. Each year, the time needed is longer, the time available shorter. Around the world, colleagues who follow different religions or perhaps no religion at all, know that everything stops in The West for two weeks and they take part in this collective deep breath. Then, like winding up a stalled clock, we all start to plan our work for the coming year, and the white boards by our office doors are covered with optimistic, colour coded to-do lists. 

Last year, one of the items on my hidden list was this blog. It's difficult to decide if I am satisfied, because I didn't know what would emerge from my own imagination and memories, or from the readers who stumble across my words. We'll see how this modest ripple behaves and if it survives after passing over the sandbar between now and the new year.

Getting things wrong

Comet ISON stumbles on after its closest encounter with the Sun (public domain, NASA, from Wikipedia).

As this is written, we are waiting to see if Comet ISON will come out from behind the sun. Two nights ago on our national news, the comet was declared dead and disintegrated, based on images taken from satellites orbiting at appropriate angles as it made its closest pass to the sun. The comet disappeared. Then a few hours later, like the dead man in Monty Python's Holy Grail who announces he'd like to go for a walk, the comet popped out of the solar glare, dimmer but at least somewhat intact. It was fascinating to watch the scientific press in the months leading up to this event.  Pessimists were adamant that the comet was doomed, while optimists anticipated the Comet of the Century. 

Is it surprising that people are confused when scientists disagree? It doesn't bother scientists much, because we live in a culture of controversy, criticism and differing interpretations of the same data. This is lost when our musings are translated for retransmittal by the media. Uncertainty, chaos and risk are elements of modern science, but much of modern society, including many science journalists and their readers, seems stuck in a binary world of plus or minus, black or white, right or wrong.

A few months ago, I read a book by Matthew Cobb called Generation, and was struck by a paragraph that accused scientists of only telling stories of success and omitting the false turns and dead ends they encounter in the pursuit of the truth. This leads to the impression that science is invariably a triumphant progression from one discovery to the next. Generation is the story of how science figured out where babies came from. It is an alternately horrifying and hilarious read, centred around two 17th century Dutch scientists, Reinier de Graaf and Jan Swammerdam. They were best buddies as students in Leiden, but became terrible enemies as they competed to work out what contribution ladies made to procreation, what Fallopian tubes and ovaries were for, and what those newly discovered squiggly sperm cells made by male mammals were about. Some scientists of the time suspected ladies might make eggs, but they imagined eggs like those of chickens, and they couldn't find anything like that in there. The vicious rivalry between de Graaf and Swammerdam shows us that 'scientists behaving badly' is not just a modern phenomenon. Both men made huge contributions, both made lots of mistakes, and they never missed an opportunity to try to squash each other.

There are many books intended for the general audience built around mistakes made by famous scientists. They tend not to illuminate the scientific process, but rather mock 'so-called geniuses' for making 'bone-headed mistakes.' John Glassie's book, A Man of Misconceptions, is a biography of the seventeenth century German Jesuit priest Athanasius Kircher, a polyglot and polymath who lived most of his life in Rome. He wrote huge volumes of natural philosophy before the scientific method was widely understood. Among his many interests was the mathematics of music, and he is often associated with the notorious cat piano (in German katzenklavier), a keyboard that pricked tails of restrained cats who were selected to howl in pitch. Kircher was controversial even in his own time because of his wild claims about magnetism (his explanation for most phenomena), his dubious translations of hieroglyphics on Egyptian obelisks, and his monographs on China, produced without the tedious necessity of actually travelling there. My favourite Kircher creation is his theory of everything, which states that there are 371,993,326,789,901,217,467,999,148,150,835,200,000,000 possible concepts. He derived this number from a formula involving the nine essential attributes of God, i.e. goodness, magnitude, duration, strength, wisdom, will, power, truth and glory; the nine universal subjects, namely God, angels, heaven, elements, man, animals, vegetables, minerals and numbers; and nine principles of relationship, being difference, agreement, opposition, beginning, middle, end, majority, equality and minority. He did this without an electronic calculator or computer, of course; it must have taken awhile. The book is predictably ironic and mocking, but not as funny as one might expect. The best joke is a cover blurb characterizing Kircher as a cross between Leonardo da Vinci and Mr. Bean. The book needed less da Vinci and more Mr. Bean.

Just as in life, making mistakes in science is an important part of getting things right. We usually don't go around bragging about our failures in life, and scientists usually don't dwell on failed experiments or half-baked ideas. Is this dishonest? Is this concealment? I don't think so. We tell our children about some of our false steps along the path of life, hoping to protect them from some pain, and scientists tell their students about the flasks that exploded, acids accidentally spilled, or experimental controls that were poorly conceived. We just don't talk to reporters about it.

The media don't consider that making mistakes in science is part of the routine. It is far more exciting to cast innuendos about competence, deception, or (hold on to your hat) fraud. In such an environment, throwing Italian geologists in jail for failing to predict earthquakes actually makes sense. But revised understanding is rarely a correction of fraud, incompetence or stupidity. It is usually compensation for incompleteness, sometimes because of laziness, but more often, limits imposed by existing technology. Each generation exceeds the achievements of the previous, not because of superior intellect, but because of refined technology. My most esteemed colleagues did not get everything right; some major breakthroughs were mostly wrong. But these inspired, energetic leaps brought us much closer to the truth, and emphasizing that they missed the target by a few percent misses the point. The story, as always, is ingenuity, insight and creativity. We get things right by first getting things wrong, just less wrong with each step.

PS. Sadly, regarding Comet ISON, the pessimists prevail and most of us will not have a chance to see its ghost in our evening skies this December. Unless, of course, we have access to some highly refined, modern technology.

Sacred literature

When I was a kid, my brother-in-law the chemist would often refer to "The Literature." He gave the phrase a reverent emphasis that at first I attributed to his British upbringing. He was disinterested in the mundane, lower case literature that most people associate with the word. He only read books of facts and hadn't read a novel since high school. I now know that when you mention The Literature to a scientist, or any academic, it means journals and books they absorb while drinking coffee or sitting on the toilet. Normal people cherish real literature that is read and reread, bought in hardback after first reading in paperback. Scientists have The Literature that is never reshelved because it is always being used. For each of us, there is the bible of our brand of biology or physics or chemistry. You might expect these to be well-known theoretical works such as Darwin's On the Origin of Species, but they are usually textbooks used for introductory courses, or reference books used in the lab.

In my undergraduate years, the bible of biochemistry was the textbook by Albert L. Lehninger called Biochemistry, then in its 2nd edition, succeeded by the title Principles of Biochemistry, now in its 6th. The most recent editions are no longer actually written by Lehninger, who died in 1986. Such is the power of his name that it is now incorporated into the title. Lehninger was an unusual textbook because you could actually read it; the man wrote good prose. Having had a childhood interest in real literature with a touch of dyslexia with peoples' names, when I picked up this textbook, I always thought of the famous short story Leiningen versus the ants. I imagined Albert L. Lehninger chasing giant ants, threatening them with biochemistry, or perhaps crushing them with his book. My own copy of Lehninger followed me faithfully for years, despite its heft, until I finally left it behind on one of my transatlantic moves. Then I bought another copy in a used bookstore for $1.50. It is still in the lab.

One science bible you definitely could not read was The CRC Handbook of Chemistry and Physics, now in its 94th edition. Its merit is proportional to its weight, now 8 pounds for all its 2668 pages. Owning a personal copy was a badge of honour for chemistry students. You could use it to look up, for example, the melting point of sodium chloride, or the molecular weight of molybdenum, to seven or eight decimal places. If you had this book full of tables and graphs, you might use it two or three times a year for class assignments and save yourself some trips to the library. A new edition is released every year, but I don't know anyone with two copies. Somewhere in the United States, there must be a house made entirely of copies of the so-called rubber bible. 

The absence of a big biology bible on my shelf is surprising. There are bibles for subfields, but for the broad subject, nothing. I can hardly remember the textbooks we used. They were uniformly tedious, turgidly written with boring grayscale illustrations that captured none of the glory of the living world. Biology always had a reputation for its heavy emphasis on memorization. You had to just know the answer for a test, and couldn't work it out with formulas or logic. Nowadays, with colour digital photography, ebooks and lavishly illustrated websites, the potential exists for a biology bible that is something other than a book. But first biologists need to escape their database rut and find a format that lives and breathes.

Many scientists hope to write their own bible some day. Most of us shuffle along scribbling scientific pamphlets and comic books, or obscure blogs. But the ultimate dream is to produce such a staggering work that our successors continue to update it in perpetuity, including our name as part of the title as they have done for Prof. Lehninger, ensuring our productivity from beyond the grave.

Lack of control

Randy's desk was closest to the lab door, so he had the first chance to say, "Hi!" to anyone who peaked in. There were many female visitors attracted by his skillful, equal opportunity flirting. He believed in the seductive possibilities of backgammon, introducing each new challenge with, "Surely there's time for one game. You can be white for purity and innocence. I'll be black."

One unusual day, the visitor was male. "Are you Randy?" he asked.

"I could be under certain circumstances."

The man held out his big, worn hand. "I'm Fred. Gerry McIntyre gave me your name." Randy relaxed, relieved that this was not a slighted boyfriend in search of revenge. "I've recorded an album," Fred said. "I need someone to do an experiment to prove my music is good for plants."

The university was famous for its population of young people who liked to involve themselves in experiments with biology and chemistry. Fred was older, at least fifty, with a grey ponytail, a tie dye T-shirt, dull eyes, an unsmiling mouth, and long delays in his conversation.

"I recorded the album myself," Fred continued. "I played all the instruments. I can think like a plant, man. All that time, I was thinking about plants and sunshine, and the plants growing towards the sunshine, making flowers. The music captures the spirit of plant growth, man. If I can get a scientist to endorse it, it will sell like crazy. Can you help me? I need a quote for the back cover."

"Why don't you leave the album with me and I'll give it a listen?" Randy suggested, hoping for a quick escape.

"No way, sorry. I've only got one copy."

Randy sighed, realizing there was no easy way out. "How do you think we should do this?" he asked. "Have you thought about the experiment?"

"Just grow a plant with the music, man, and you'll see how great it grows."

"What kind of plant?"

"I was thinking beans. Scientists are always doing experiments with beans. I think I could get some."

"Beans would be good. But how many replicates do you want? And you'll need some kind of control."

"Replicates? Just one, man. Anything more would be a waste. I don't want to waste the beans, man."

The conversation degenerated into a circular argument. There was no way that Fred was going to waste resources on a control, and replication was a hard sell. He finally reluctantly agreed that two plants would be acceptable. Randy tried to convince Fred that without controls, that is, plants not exposed to music, it would be impossible to interpret the results. Nor could he understand the need to measure the dry weight of the plant as a measure of growth. "It's enough to just see if the plants grow better," he insisted. "Use a ruler!"

"Better than what?" Randy shouted. "How will you know the music worked?"

"Don't dry the plants," Fred concluded. "I want to make a salad with the beans."

Satisfied that he had made his point, and that we would do the experiment the way he wanted, Fred left the album behind. It was unlistenable, full of random flute sounds, bongos and what appeared to be singing. Fred was tone deaf with a indefinable sense of rhythm. But of course my opinion was irrelevant; I am not a plant.

Eventually, we found an empty growth chamber (a refrigerator-like chamber with controllable light, temperature and humidity), plugged in a record player, and put the album on automatic replay. We planted the two magic beans, grateful that Fred didn't require a second, music-less growth chamber for controls. The plants started to grow. Then they died.

"I can only conclude that your music killed the plants," Randy told Fred. 

"Did you even remember to water them, man?" Fred hollered. He grabbed his album and stomped out, mumbling that he would find another scientist to do the experiment properly, or better yet, endorse the album without wasting any more beans.

Controls are the trickiest part of experiments. If you follow research on human health, disease, or diet, the most common criticism of published studies is inadequate controls. Proper controls allow the interpretation of results to be unequivocal and unassailable. Improper controls leave you wondering whether you have proven anything at all. In science, to use a cooking analogy, if you want to be sure you've improved the cookie recipe, you have to make them the old way too so you can compare the original and the modified version side by side.

Poor Fred. We never heard from him again, and there were no rumours of a fortune from marketing his record to enhance plant growth, whatever kind of plants it was he was really interested in.

No bell prize

Last week was Nobel week, with daily announcements of the honourees. Not all of them are for science, of course. The last one was Economic Sciences. Really?

The Nobel Prize holds a prominent place in the public imagination when they think of science, sort of like the Academy Awards, the Olympics, or the World Cup. Although the prizes are considered the height of achievement, most scientists have no chance of winning one, not because they are not smart enough (we are of course all smart enough), but because they do not work on the right thing. No one in my field has ever won a Nobel Prize, although we sometimes claim reflected glory for a couple of prizes awarded to people who happened to do some experiments with organisms in the same Kingdom. Actually, there is no specific Nobel for biology like there is for physics or chemistry, but instead a narrowly defined focus on Physiology or Medicine. Others need not apply.

Every field has its awards, however, some more prestigious than others. It is not unusual to hear these major awards marketed as, "The Nobel Prize of <insert field here>." Those who win these awards, however, are not interviewed on the national news in their countries, possibly not even on their local news. It might get mentioned to the in-laws as an aside over Thanksgiving dinner, bringing an abrupt end to casual conversation, spoons frozen in mid air. Then the prize winner will again have to explain what it is he or she actually does, expecting that the niece's new boyfriend will try to score some points by quipping, "You get paid to do that?"

In Canada, real Nobel Prize winners in science do become celebrities of a sort. We don't get a lot of them here, so it's always exciting. If they have any hint of an interesting personality, Nobel laureates do well in the media by talking about things other than science, or by demonstrating that they know how to play the violin. They attend formal galas, drop the opening puck at hockey games, appear on the news when a scientific pundit is required, and complain as much as possible that there is not enough funding for scientific research.

At the Fictional Scientific Conference I attended a few months ago, I was presented with an award that no one could characterize as anything close to a Nobel Prize. The Master of Ceremonies whispered beforehand that they would prefer I not try to say anything while accepting the plaque so they could maximize the time available for the fundraising auction. I had been hoping to pretend to be a pundit for a minute or two, and say something profound, or perhaps play the guitar, but no luck there. A few friends congratulated me afterwards, but everybody else either looked embarrassed or ignored me. Even in my own esoteric field, our intellectual passions are so fractionated into subfields and subsubfields that it sometimes seems that no one is interested in anything that anybody else does. We're polite about it, but when you win the "like the Nobel Prize of <insert subsubfield here>", you won't be toasted by the King of Sweden, and the President of the Society might try to rush you off the stage.

Postscript: A proud tip of the beaker to this year's Nobel Prize winner for Literature, Canada's Alice Munro. 

Not that kind of doctor

My PhD does not get me much respect outside the workplace. The acronym supposedly means Doctor of Philosophy, but I've never taken a philosophy course in my life, so this feels wrong. We've all heard the 'Piled higher and deeper' explanation, but I always liked the interpretation of a Finnish colleague who transcribed it as 'Doctor of Photocopying', which I suppose must now be adapted to 'PDF hoarding Doctor.' The stereotype, of course, is that PhDs are clueless about the broader world, their brains having been vacuumed into a dark, narrow tunnel from which they rarely escape. The leading newspaper chain in Canada adopted the editorial policy many years ago that PhDs were not 'Dr.', but just 'Mr.'  Even professors, who in some countries are exalted as 'Prof. Dr.', or even 'Herr Prof. Dr.', are reduced to 'Mr.' by journalists who do not have university degrees.

When I first got my PhD, I was surprised by the hostility of friends and family who assumed my ego was about to inflate like a hot air balloon. They considered it necessary to constantly puncture my self esteem before I floated into the academic stratosphere, where I would gaze down condescendingly at the rest of mankind.

From the beginning, I did not use the 'Doctor' label much out in the real world. Some perverse stubbornness makes me use the title when interacting with others who use the same word as a social or intellectual stratifier, such as MDs (medical doctors), DVMs (vets) and DMDs (dentists), who mostly have fewer years of schooling than I do. The receptionists at my dentist went along with it for awhile, calling me Doctor for a year or two. They never quite believed I was a real doctor, possibly because I never wore a tie or stethoscope. Eventually, they started using just my first name, not even bothering to call me Mister. I don't mind, really, although at the end of this month l will be introduced to a new MD who will do unspeakable things to my body. His web reviews suggest an arrogant, imperial personality, certain to introduce himself as Doctor if he bothers to introduce himself at all. I'm sure I will introduce myself as Doctor in return.

I immersed myself in universities for nine years to get my PhD, but it still feels odd when people outside my field call me Doctor. It's a symbol of something, an accomplishment, the development of expertise that really is unique, but it is not something I did because I wanted the title. It was a side effect, not the reason, a signpost hammered in along the road, now far far behind me. After awhile, people stopped caring about the letters after my name, whether they be PhD or CSP (Clown Science Practitioner). What is important, now,  is how well I do the job, not whether I have the academic credentials to make you laugh.

The thesis defence

Tomorrow, I sit as an examiner in a Master of Science thesis defence. The student worked for two years on a complex, original piece of research, and a month ago delivered 100 pages of text and figures and tables for dissection by committee. His defence is imminent, and he is probably now descending into the bowels of panic, and may not sleep until it is all over. We cannot give any indication, right now, that he has done a splendid job. The sweat is part of it. 

The thesis defence is a narrow doorway that most in science must squeeze through at least once, the hounds of academia snapping furiously at their butts. To earn a PhD, you may have to go through it a second or even a third time. It is terrifying. You work for two years or five years or ten years on some obscure topic, transcribing results from lab books or post it notes, refabricating what you neglected to write down as it happened. Then you stand in a room before a group of professors whose job is to attack. Attack you and what you wrote. Attack all those years you worked. Attack your logic and your ability to express yourself. Attack the way you look, the way you speak, your clothes, your friends, your ...

At the first PhD defence I attended, wanting to witness such a confrontation before enduring it myself, the candidate was asked, "Can you relate your results to the persecution of Jews in Nazi Germany?" After agonizing hesitation, the student found the right answer, a respectful "No." Then he faced a second examiner who was clearly drunk, who thought the whole thesis was based on flawed ideas and a complete waste of time. After several hours, most behind closed doors away from the public eye, the student emerged successful. He had just 24 hours to make the required changes to his 400 page opus because he had a nonrefundable flight to return to his wife and kids. This was before word processors. He had to retype complete pages, or insert previously typed pages into the typewriter and wriggle them around until the letters lined up so that he could type over the original lines, which were painted over with White Out. He did not have the luxury of sleep after his defence.

My own MSc thesis defence is not even a blur, it is obliterated from my mind. I only recall standing in the hallway afterwards, waiting for the profs to pass judgement, a condemned man waiting for the gallows. Other students passed me in the hallway, but none made eye contact. I realize that I must have gone through the standard routine and given a ten minute summary of my research. The examining committee took turns grilling me, twice around the table. I don't remember the questions or the answers, only the overwhelming feeling that it needed to be over as quickly as possible.

The memories of my PhD defence are much clearer. In Europe, it is a public event attended by your family, friends and colleagues. The formal rituals, processions of professors in robes and mortar boards, my own tuxedo and the dresses of my female colleagues, amused me greatly. Unlike Canadian defences, which go on for hours, the six examiners had only 48 minutes to attack me and my work. After my brief presentation, I used up ten minutes with a verbose, meandering answer to the first question, to the horror of my supervisor, who was signalling me to shut up. The next examiner focused his interrogation entirely on details from one page, obviously the only one he had read.

Since then, I've been the supervisor, the ordinary committee member, and the external examiner. As supervisor, you are defending your academic child, aware that the quality of your mentorship is being evaluated by the board more than the quality of the thesis. As a committee member, you usually don't understand the thesis very well, and try to ask questions that won't reveal to the student or the supervisor that you are a complete ignoramus. The external examiner function is even weirder; you were not involved in the research at all, and are invited to provide an impartial assessment. You are an expert but a stranger; the reputation of the university, the department, the supervisor, the committee and the student are on the line. If you don't praise the thesis, they will hate you.

Everyone sits in the examination room, playing their role. The student is the focus, everyone is actually on his or her side, but the student believes everyone is the enemy. They emerge feeling attacked by lions in a coliseum, academic limb torn from academic limb. Rationally, they know that if the thesis was inadequate, they would never be allowed to defend. But that doesn't count for much when you hear teeth snapping in your face and smell that rabid academic breath.

Tomorrow, everyone but the student knows that this thesis will pass, and that a Master of Science degree is certain for this bright and happy young man. Hopefully, the trauma will not discourage him from a life in science. I hope he will join us on the dark side, but don't expect an invitation to the party afterwards.