Taxonomic Technology: Electrophoresis & Classification in Agricultural Botany (Part 1)

My second ever work-in-progress seminar at the University of Leeds introduced attendees to the second chapter of my PhD, which examines the use of laboratory machinery and biochemical methods to identify and analyse crop varieties at the National Institute of Agricultural Botany (NIAB) during the 1980s. By the late-twentieth century, classifying agricultural plants was a difficult task. More and more varieties were submitted to NIAB by plant breeders, while the distinguishing characteristics of varieties grew smaller and smaller. Identifying and classifying varieties had traditionally relied upon botanically-trained observers. Yet visual scrutiny of plants’ morphological characteristics was problematic, requiring both considerable expertise and grown specimens.

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The problem of classifying of agricultural plants is demonstrated by these images of celery varieties. Each column here represents a distinct variety: the correct classification of these samples by eye would be a near-impossible task for the untrained observer. From G.W. Horgan, M. Talbot and J.C. Davey, ‘Plant variety colour assessment using a still video camera’, Plant Varieties and Seeds (1995) 8: 161-169.

An escape route was provided to NIAB via a form of protein fingerprinting developed in biochemistry: electrophoresis. For historians of biology, electrophoresis is best known for its use by Lewontin and Hubby to break an impasse in population genetics during the 1960s. Electrophoresis was trialed at NIAB during the same period, to little avail. Matters changed during the early years of the 1980s, when staff at NIAB’s Chemistry and Quality Assessment Branch were able to apply electrophoresis to cereal varieties. Electrophoresis works by running an electric current through a gel in which a sample sits. As different proteins carry different charges, they separate into distinct “bands” (see below).

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An early image of a completed electrophoresis sample. The darker protein “bands” can be seen once the gel is chemically dyed. From R.P Ellis, ‘The identification of wheat varieties by the electrophoresis of grain proteins’, Journal of the National Institute of Agricultural Botany (1971) 12: 223-235.

Electrophoresis provided a new means of classifying agricultural plants and was promoted in NIAB’s publications as an efficient and modern technique of variety identification. The experience of the Institute during the 1980s chimes with what historians of science have termed the “molecularisation movement” in the life sciences. This movement is usually associated with genetics and the role of DNA and nucleic acids. Yet historians have called for broader studies under the theme of molecularisation, not least because of the broad use of terms such as “molecular biology” by scientists themselves. Financial gain and prestige came from NIAB’s research into electrophoresis; the technique still appears in guidelines issued by international agricultural bodies today, despite the rise of DNA sequencing. Yet electrophoresis was not the only method of classification investigated by NIAB during the 1980s, as future posts will explore…

 

 

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Gregor Mendel & Scientific Fraud: iHPS Workshop, University of Durham (Part 2 of 2)

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On the second day of the iHPS workshop at the University of Durham, Professor Greg Radick (University of Leeds) delivered his keynote address “Is Mendel’s Evidence “Too Good to Be True”? This year has seen the one hundred and fiftieth anniversary of Mendel’s two 1865 lectures “Experiments in Plant Hybridisation,” with many drawing a line directly from Mendel’s findings to modern biotechnology. Yet two ghosts exist at the Mendelian feast: the specter of eugenics and the accusation that Mendel fraudulently obtained data. Or as Ronald Fisher termed it, that Mendel’s results were “too good to be true.”

Mendel’s 1865 findings are known to many of us. Hybridising garden peas in his monastery garden revealed a reoccurring pattern of three-to-one in second-generation hybrids. In later generations, traits reversed, with gametes receiving heredity information randomly. If we flip a coin multiple times and always end up with an exact fifty-fifty split, eyebrows would be raised. In a 1902 paper by W.F.R. Weldon, statistical analysis of Mendel’s data revealed such a trend, as the latter’s result accorded remarkably with his hypothesis. The chances of Mendel arriving at his results by pure coincidence was placed by Weldon at sixteen-to-one. In 1911, Ronald Fisher spoke at the Cambridge University Eugenics Society on Weldon’s findings. By this time, Mendelian genetics has been established beyond controversy and integrated with Darwinian natural selection. At this talk and in a later 1936 paper, Fisher declared that Mendel regarded his experiments as an empirical demonstration of his conclusions. Mendel was no mere experimentalist – though his results were still fake. Fisher laid the blame at the feet of one of Mendel’s assistants, who had doctored experimental results to please his master.

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Drawing upon affair, Professor Radick noted that Mendel’s peas were not intended to be “true-to-nature,” but represented absolute qualities. For historians of science, the episode suggests that a more thoughtful, systematic approach to scientific fraud is needed. We should also be aware of different approaches to genetics offered by historical figures such as Weldon, who emphasised the interaction of genes with each and other and the environment. In fact, recent results from Leeds HPS Genetic Pedagogies Project suggest that students placed on a Weldonian-style genetics course emerge less convinced of genetic determinism than their Mendelian peers.

Field & Laboratory – Darwin in the Ottoman Empire – Chinese Biology & Goldfish

Other associates of Leeds HPS also presented well received papers on the history of biology. Cultivating Innovations (http://www.cultivatinginnovation.org/) postdoc Dominic Berry (@HPSGlonk) spoke on the historical division of field and laboratory, drawing upon randomised control trials at the National Institute of Agricultural Botany (NIAB). Visiting fellow Alper Bilgili (@BilgiliEnglish) described the reception of Darwinism in the Ottoman Empire. Darwin was enthusiastically embraced by some westward-leaning Turkish intellectuals who greatly admired the scientific method – while others sought to integrate Darwinism with traditional religious beliefs. Lijing Jiang (@LijingJiang), who (all too briefly) visited Leeds for some weeks, spoke on Chinese biologists’ investigations into genetics and evolution from the early-twentieth century. In contrast to the experimental cultures of many Western universities, Chinese biologists who studied native goldfish drew upon historical accounts to reconstruct the animals’ evolutionary past.

Book Review: The Future of Scientific Practice: ‘Bio-Techno-Logos’

This eclectic volume emerged from discussions between members of the Bio-Techno-Practice (BTP) think tank at the University Campus Bio-Medico in Rome. Its authors found reoccurring questions in their discussions on cancer, other complex diseases and systems biology. These included the ubiquity of “bio” as a prefix, the dichotomy of reductionist verses systemic views and progressive convergence of explanatory systems, in fields ranging from ecology to robotics. Each contribution in this volume is linked by the relationship between “Bio” (the biological or physical world), “Techno” (how we conceive this world, through software, instruments or scientific paradigms) and “Logos” (our scientific understanding and representation of the world). Three chapters out of eleven are discussed below:

Embodied Intelligence in the Biomechatronic Design of Robots – Dino Accoto, Cecilia Laschi & Eugenio Guglielmelli

Lee Model 6A Manipulator on mobile platform, c. 1974: http://cyberneticzoo.com/tag/1960s/

Robotics is a young discipline – the first modern robot was installed in a New Jersey General Electric plant in 1960. Today, robot design can be based on a “biomechatronics” approach – combining information and methods from control engineering, mechanical engineering and the life sciences. The result is “bioinspired” or “biomimetic” robots, better able (in theory) to negotiate uncertain, real-world environments. Intriguingly, this approach builds on Norbert Wiener’s 1943 conception of cybernetics, “a unified approach to the study of living organisms and machines.” Practical results include octopus-like robots displaying “embedded intelligence” and wearable robots imitating symbiotic organisms.

Managing Complexity: Model-Building in Systems Biology and its Challenges for Philosophy of Science – Miles MacLeod

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Schematic showing high-confidence protein–protein interactions between NANOG and NANOG-associated proteins. From “Systems biology of stem cell fate and cellular reprogramming,” Ben D. MacArthur, Avi Ma’ayan & Ihor R. Lemischka. Nature Reviews Molecular Cell Biology 10, 672-681 (October 2009): http://www.nature.com/nrm/journal/v10/n10/fig_tab/nrm2766_F1.html

Systems biology is described by MacLeod as not “normal science,” posing distinct challenges for philosophers of science. Based on a five-year ethnographic study of two systems biology labs, MacLeod claims that systems biology (loosely defined as an attempt to model complex biological systems using computers and mathematics) positions itself against other biological fields like molecular biology. The former uses “mesoscopic modelling,” neither a “top-down” nor “bottom-up” approach to biology, above the molecular level but incapable of encompassing biological phenomena like disease. Systems biologists are ambivalent about general theories of biological systems and often pursue different modelling agendas. Methodological and epistemic diversity define the discipline. As such, a philosophy of scientific practice that explains how this diversity trades off against disciplinary certainty and approaches to handling complexity is required to encompass it.

Teleology and Mechanism in Biology – Marco Buzzoni

A prevailing brand of thought in the philosophy of biology is that the teleology (or purpose of) organisms can be explained by empirical forces which are themselves not intrinsically teleological. A real-world example would be August Weismann’s claim that the “philosophical meaning” of Darwinism is found in the principle that evolution “does not act purposefully, but nonetheless brings about what is suitable for an end.” This mechanistic approach dispenses with both nineteenth-century reductionism and the positivist unity of science. Yet Buzzoni declares that a mechanical investigation of life cannot dispense with teleology or final causes. Teleology is not only essential to causal imputations, but acts a powerful “heuristic-methodical device” to investigate biology in a testable and reproducible way. Purpose should not be excluded from the scientific-experimental investigation of biology, as this assumption makes it possible to examine mechanical, physio-chemical laws and connections in organisms.

Although complex in some areas, The Future of Scientific Practice tackles significant hurdles in the philosophy of biology, while firmly grounding itself in contemporary science.

Marta Bertolaso (ed.) The Future of Scientific Practice: ‘Bio-Techno-Logos’ (London: Pickering & Chatto, 2015) is available in hardback and as an ebook (£24 incl. VAT for PDF, £20 excl. VAT for EPUB) at: www.pickeringchatto.com/BTL

 

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Experimental and Speculative Hypotheses in the Seventeenth Century: Integrated History & Philosophy of Science Workshop, University of Durham (Part 1 of 2)

Last Thursday and Friday saw the 10th annual UK Integrated History and Philosophy of Science Workshop (IHPS) take place at the University of Durham. One solid attempt to combine the two fields was made by Catherine Wilson (Professor of Philosophy at the University of York) in her plenary talk, which addressed seventeenth-century notions of a “hypothesis,” with a focus upon the early life of the Royal Society.

Experimental and Speculative Revisited: What was Behind the Rejection of “Hypotheses”

Early modern England saw a series of methods applied to natural philosophy, which manifested themselves in observational and experimental reports, or more speculative natural philosophy. Texts from the Royal Society disparaged the former,  causing some historians to theorise that the empirical and rational debate in philosophy stemmed from this period. The problem with speculative philosophy, as seen by members of the Royal Society, was its association with Cartesianism and Epicurean philosophy. Distinctions between practical and speculative philosophy are very clear in seventeenth-century letters. Even theologian Richard Baxter weighed in on important of use in knowledge. Natural philosophy was a multi-sensual and instrumental enterprise, the complexity of which naturally led to group work in Italy, France and England.

Philosopher John Locke spoke on both distinctions, but without denigrating the speculative, as was also the case with Francis Bacon. Corpuscularianism (that matter is composed of minute particle) was popular among Royal Society members, encouraging both approaches. Robert Hooke’s observations in his Micrographia were combined with speculation on invisible mechanisms, which were not subject to experimentation. Hooke was actually keen to be seen as a philosopher, rather than a mere “mechanic.” The activities of leading Royal Society members contradicted the Society’s publications criticising speculation.

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Hooke’s drawing of a flea viewed under his microscope, “adorn’d with a curiously polish’d suite of sable Armour, neatly jointed.” See: https://scolarcardiff.wordpress.com/2012/08/30/life-through-a-lens-exploring-the-miniature-world-with-robert-hookes-micrographia/

Even critics of Cartesianism speculated on invisible forces. Descartes’s famous drawing of the magnet mechanisms was similar to the speculations of figures such as Newton, Hooke and Boyle. As medieval scholastics were displaced by the new natural philosophers, experimental philosophers required the corpuscular hypothesis to rise above the level of messy craftsmen and mechanics. But when speculation ran too far ahead of experiment, it was criticised as “Vain” or even “Pagan” philosophy, which neglected spiritual and providence to get at rudiments of nature. Bishop Stillingfleet’s 1663 work on the doctrine of the self-formation of world condemned Epicurean philosophy and those who deceived others with hypothesis based on tradition, not from “experiments of nature.”

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Descartes: Striated particles (particulae striatae) pass veins inside the earth in two senses: http://www.journalfuerkunstsexundmathematik.ch/category/magnes/

Epicurean and Aristotelian philosophy became associated with dreaded “atheism.” Robert Moray even declared a ban on investigation into “original causes” by Royal Society members. Descartes’s claim that everything could be explained by laws of matter and motion was a worse sin. Natural philosophers were now expected to state that nature implied a benign god. Newton’s condemnation of atheism began with a criticism of Cartesian vortex theory: by refuting the mechanical base of the system, he could refute atheism. Newton’s own worldview required divine intervention, if only to stop the planets crashing into sun. Gravity was part of a divinely-fashioned order, not an intrinsic property of matter.

When Darwin’s On the Origin of Species was published in 1859, he faced a more hostile reaction in England than elsewhere. European and Scottish philosophers had addressed questions beyond the “veil of nature,” including original causes. In England, an old alliance of theology and naked-eye empiricism attacked the speculative aspect of Darwin’s theory, which linked contemporary breeding with natural history.