Pasteurizing the truth? Why even the best scientists need an ELN

Did you know?

Louis Pasteur is famous for his many contributions to medicine and science. His image is held high as a benevolent, bearded beacon of scientific integrity and his grandfatherly face looks down approvingly from dog-eared middle-school science classroom posters around the world. Although it may be hard to open a bottle of milk without being reminded of Pasteur’s many accomplishments, details of the specifics of his day-to-day research remained sketchy for many years after his death. It turns out that Pasteur was a somewhat complex and secretive man who fiercely protected his notebooks and apparently believed in neither research transparency nor peer review as we understand it today. In fact, his original laboratory notebooks did not become available for public scrutiny until the 1970s.  In his 1996 book The Private Science of Louis Pasteur, Dr. Gerald L. Geison examines Pasteur’s life and legacy as it is revealed through his original research notes and writings. His conclusions are somewhat surprising, even unsettling, as Geison identifies a number of serious discrepancies between the procedures and results Pasteur reports in his laboratory notebooks and his public claims and pronouncements. In some cases, Pasteur borrows procedures from others and claims them as his own. In other more serious cases, Pasteur appears to make some reckless medical decisions based on scant research data. To his credit, the outcome of these cases was invariably favorable, but in modern times, medical treatment that amounts to experimentation on human subjects would be considered unethical or even criminally negligent. On the other hand, we should exercise caution when judging the actions  of past scientists through the lens of modern medical regulations and standards, and as Geison points out, although there are some discrepancies between Pasteur’s public and private writings, his lab notebooks still reveal exceptional skills as an experimentalist and theoretician. The fact that he kept a laboratory notebook at all also reveals an earnest desire to faithfully and empirically pursue answers based on real scientific observations.

 A fascinating review of Geison’s book in the New York Times includes some interesting reflections by some of Pasteur’s modern-day colleagues on the importance of the lab notebook:

“If a scientist's papers are correct, confirmation comes from others who repeat the experiment. But it is when they cannot repeat what you have published that you had better have good notebooks so you can go back and find out a reason for the discrepancy," said Dr. Jay Levy, an AIDS researcher at the University of California at San Francisco.
"With all the investigations done now, I emphasize to my lab that someone might need to come here to look at a notebook, and that is why none is allowed to be taken out of the lab," Dr. Levy added.
That rule was strictly enforced only after a researcher was mugged on his way home from work and had a notebook stolen. "He held on to his backpack so much that the robbers thought it had something of monetary value," Dr. Levy said. The notebook was never recovered and the scientist had to spend several months repeating his work.”

External Links:

http://query.nytimes.com/gst/fullpage.html?res=990CE5DD173DF935A25756C0A963958260&sec=&spon=&pagewanted=al

Those diligent Darwins and their family tradition of scientific notebooks

Did you know.... ?

2009 marked the 200th anniversary of Charles Darwin’s birth, and it seems fitting to mention here his diligent and invaluable use of field notes and diaries to record his thoughts, ideas and research. His original handwritten notebooks are lovingly preserved at Down House in the UK and much of his work is now freely available online. Generations of science historians have delighted in tracing the observations and lines of argument that eventually led to the publication of On the Origin of Species  in 1859, and even today, reinterpretations of his original data and notes continue to reveal new insights. Charles 

Darwin’s notebook-keeping habits owe much to his grandfather, Erasmus Darwin, who was a medical doctor as well as a prolific thinker and inventor. Erasmus belonged to an informal group of scientifically inclined gentlemen called “The Lunar Society,” widely recognized as a major catalyzing force behind the industrial and scientific revolutions of the 18th and 19th centuries. Darwin never knew his grandfather but was familiar with his works, especially his scientific ideas, which Erasmus recorded in his detailed and elaborately cross-referenced “commonplace book,” an early forebear of today’s modern lab notebook. Erasmus was so sophisticated with his record keeping and cross-referencing methodologies that we can be sure that as far back as the 18th century there were great scientists who understood the value of data mining, and the inadequacies of linear notebooks as a storage medium. Erasmus went to great lengths to try to help those thinkers that might one day read his work and attempt to build upon it, and as it turns out, this was extremely useful for his famous grandson. 

Charles was profoundly influenced by his grandfather’s ideas about evolutionary biology. We know this because Charles Darwin’s copies of his grandfather’s publications still exist and many have been clearly and thoughtfully annotated in Charles's own hand. For example, next to a paragraph where Erasmus describes the way that birds’ beaks may have diversified as a result of the birds’ own endeavors to find food, Charles wrote:

"Lamarck, concisely forestalled by my grandfather"

Elsewhere, Erasmus describes farmers’ selective breeding of sheep with favorable traits as a way to to improve the flock. Charles writes "Good" showing his preference for the idea of selection rather than "modification by endeavor" as a mechanism for change.

This is a great example of what Isaac Newton called "standing on the shoulders of giants"; the process of learning from the records of those who have proceeded us, and building upon their work. The usefulness of this process in modern science should never be underestimated. Lev Vygotsky famously said that all learning is social, but how do we socially interact with people who are no longer living? The answer is that we can have a dialog of sorts with them by studying the work that they have left behind, and this dialog is most meaningful when the work they have left us is richly annotated in ways that help us understand their thought processes and ideas. Luckily for us, This process of rich annotation of thoughts and activities was very a deeply engrained habit in multiple generations of the Darwin family.

Bibliography:

Darwin, C., Krause, E. (1989) "Erasmus Darwin, The Biography of Erasmus Darwin with a Preliminary Notice by Charles Darwin” Ed. Nora Barlow. University Press 

Darwin, E. (1970) "Commonplace Book" [microform] Reproduced from the original manuscripts at Down House. New York: Distributed by Clearwater Pub.

Darwin, E. (1791) "The Botanic Garden: a Poem in Two Parts Part I: The Economy of Vegetation" London: J. Johnson 

Darwin, E. (1789) "The Botanic Garden: a Poem in Two Parts, Part II: The Loves of Plants" London: J. Johnson