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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What is a Biological Individual & Why Does it Matter?

Back in July I was invited to attend my first summer school, a gathering of young scholars at Gut Siggan in Holstein, Germany. The subject of our collective brainstorming was ‘Superorganisms, Organisms and Suborganisms as Biological Individuals’. In other words, what is an ‘individual’ in biology, how do we arrive at this definition and why does it matter? The summer school had a distinctly interdisciplinary twist, bringing in biologists, philosophers, sociologists and even a few historians – including yours truly. During the various lectures and seminars we heard varied examples from the history of microbial classification to perspectives on modern DNA testing to remind ourselves what a difficult – and often controversial – task labeling something as a biological individual can be.

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Attendees of the ‘Superorganisms, Organisms and Suborganisms as Biological Individuals: First Interdisciplinary Summer School on Individuality in the Life Sciences’, 27-31 July 2015. The organisers were Marie L. Kaiser, Thomas Reydon, Christian Sachse & Marianne Schark.

Participants were pointed to one particularly interesting piece of reading by Lynn Nyhart and Scott Lidgard ‘Individuals at the Center of Biology: Rudolf Leuckart’s Polymorphismus de Individuen and the Ongoing Narrative of Parts and Wholes’ (Journal of the History of Biology 44 (2011): 373-443). Nyhart and Lidgard point out that biological individuality was as central a problem to pre-1859 naturalists as evolution. Philosophical notions followed discoveries in cell theory, discussions on compound organisms and debates over the existence of single-celled organisms (p. 374). Zoologists like Leuckart were also involved in ongoing disputes in taxonomy, dividing and creating animal groups to create new classification systems (p. 377). In the concluding paragraphs of their paper, Nyhart and Lidgard attempt to draw parallels between modern trends in biology – including interest in modular organisms and developmental modularity – and nineteenth-century discussions of individuality (p. 406). But does the latter really possess relevance today? Do seemingly arbitrary and ever changing definitions actually make a practical difference in the world?

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Invited speaker Mathias Grote (Humboldt-Universität zu Berlin) introduces the history and philosophy of microbiology.

In a series of important contexts, yes. To take one example from my own research, getting a new breed of plant recognised as a variety can bring intellectual property protection and potentially lucrative commercial awards. Other speakers at the summer school pointed out that what we recognise as a biological individual is important in how we carry out conservation programmes; we need to know what we are actually trying to preserve. Yulia Egorova, a lecturer from the University of Durham, revealed the impact of DNA testing on cultural and religious groups. How we perceive human individuality can often have dangerous consequences for how we view ourselves and others. What constitutes a biological individual is not simply a question best left to philosophy.

Molecular Biology and Evolution at ISHPSSB 2015, Université du Québec à Montréal

The Blog is Back! Following a few hectic weeks of international travel, including the International Society for the History, Philosophy and Social Studies of Biology (ISHPSSB) 2015 conference in Montreal, normal service can resume. ISHPSSB was the first international conference I had ever attended. With hundreds of attendees, it was also the largest! Nominally I was there to present a paper on a facet of my PhD research – the history of a largely ignored form of biotechnology know as somatic hybridisation (http://leeds.academia.edu/MatthewHolmes). But with multiple panels and sessions, ISHPSSB’s speakers were delving into everything from Darwin to embryology, ecology to agriculture. One of the most intriguing (and popular) panels discussed aspects of molecular biology and the modern synthesis in biology. As always, a few textual snapshots are provided below:

But first, some Montreal landmarks…

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Vassiliki Betty: The modern evolutionary synthesis brought together botanists, geneticists and paleontologists under a single conceptual framework – one which combined evolutionary ideas and Mendelian genetics – during the mid-twentieth century. By the end of 1950s, advocates of the synthesis was arguing for evolution as the unifying theory of biology. Links between chemistry, physics and biology also grew as biologists jumped on the ‘DNA bandwagon’. Yet all was not well in the new world of biology, as rifts between the new molecular biologists and traditional organism-focused biologists occurred in American Ivy League institutions. One well-known example is found in E.O Wilson’s memoirs, which described his Harvard colleague James Watson (co-discover of the structure of DNA) as the ‘Caligula of biology’, who aggressively drove the molecularisation of biology and even blocked the appointment of ecologists to the department.

Yet other noted figures felt no such clash. Botanist George Ledyard Stebbins Jr. embraced the techniques of molecular biology by the mid-1950s, despite his training in taxonomy and museum work. Chair of Genetics at UC-Davis during the 1950s and ’60s, Stebbins encompassed developmental genetics (which challenged Mendelian genetics) and postulated new mutation processes, including the easier formation of inter-specific hybrids in plants. In a 1968 paper he stated that modern synthetic theory was based upon multiple disciplines and acknowledged there were different answers to how characteristics – for example the neck of a giraffe – developed, given by field naturalists, Darwinians, developmental genetics and molecular biologists. None were wrong. All were correct, but incomplete.

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ISHPSSB President Michel Morange speaks to a packed room at the molecular biology session.

Michel Morange: Jumping to the mid-1980s, molecular biologists had accepted evolutionary synthesis, as the Luria-Delbrück experiments chased Lamarckianism out of microbiology. Molecular biologists used Darwinism in their work, isolating mutations to demonstrate the creative power of variation and selection. François Jacob (1982) stated that embryonic development had been ignored. But various molecular biologists continued to have ideas about the molecular mechanisms of evolution. Research was not always straightforward. The T-complex model, proposed by Dorothea Bennett in 1975, was supposed to demonstrate how embryonic development of mice was disrupted. Unfortunately the T-complex turned out not to exist. Yet other models, including gene regulation and  heterochronic mutation were successfully integrated. It is now acknowledged that there are different forms of evolution and progress in evolution occurs independently of the environment. The molecular biologists were largely Darwinian but did not follow the evolutionary synthesis to the letter.

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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