Comparisons – Page 12 – Science-Education-Research

proteins act like molecular swivels or molecular hinges

An example of a similes used in explaining science:

"'Binding of the spectrin lattice to the cytoplasmic domains of the transmembrane proteins is mediated primarily by two multifunctional proteins, protein 4.1R and Ankyrin…. Each of these molecules has separate binding regions for the cytoplasmic domains of transmembrane proteins and for the spectrin-actin cytoskeleton. They thus provide strong yet flexible attachment, much like "molecular swivels" or "molecular hinges," conferring the freedom of motion needed for the twisting or sliding of the cytoskeleton across the inner surfaces of the phospholipid bilayer when the cells are distorted by shear stress and stretched or shrivelled by osmotic changes."

Benz, Edward J. (2018) Anemias, Red Cells, and the Essential Elements of Red Cell Homeostasis, in Edward J. Benz, Nancy Berliner, & Fred J. Schiffman, Anemia. Pathophysiology, Diagnosis, and Management, Cambridge University Press, 1-13.

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erythrocyte membrane cytoskeleton protein is like a spring

An example of a simile used in explaining science:

"Fortunately, the erythrocyte membrane cytoskeleton is uniquely adapted to circulate in that vasculature. The underlying protein scaffold consists primarily of spectrin. Spectrins are large (ca250 kD [kilodalton]) helical proteins. In erythrocytes, the functional unit of spectrin is a dimer of α spectrin and β spectrin. These chains bind to one another in a head-to-tail fashion in such a way as to become entwined along a series of more than 20 helices. This structure allows the protein to be highly extensible and compressible, roughly like a spring."

Benz, Edward J. (2018) Anemias, Red Cells, and the Essential Elements of Red Cell Homeostasis, in Edward J. Benz, Nancy Berliner, & Fred J. Schiffman, Anemia. Pathophysiology, Diagnosis, and Management, Cambridge University Press, 1-13.

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haemoglobin becomes more avid for oxygen

An example of anthropomorphic language in medical writing:

"…at low oxygen tensions, hemoglobin has a low affinity for oxygen until the oxygen concentration is sufficient to break so-called salt bridges that would otherwise bar access of oxygen to the iron moiety within heme. This binding shifts the configuration of heme molecules within the remaining chains of the tetramer to make the breakage of those salt bridges easier. Thus, as oxygen tension rises, the hemoglobin becomes more avid for oxygen, and the amount of binding increases steeply over a relatively narrow range of oxygen tension. In other words, 'binding begets more oxygen binding'."

Benz, Edward J. (2018) Anemias, Red Cells, and the Essential Elements of Red Cell Homeostasis, in Edward J. Benz, Nancy Berliner, & Fred J. Schiffman, Anemia. Pathophysiology, Diagnosis, and Management, Cambridge University Press, 1-13.

Avis refers to a keen interest or enthusiasm, perhaps approaching greed.

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Many examples of anthropomorphism are listed in 'Creative comparisons: Making science familiar through language. An illustrative catalogue of figurative comparisons and analogies for science concepts'. Free Download.

The positive feedback ('cooperative binding' – see 'haemoglobin is like a four-seater car or an unstable four-man boat') is described metaphorically as 'binding begets more oxygen binding' where beget is perhaps most familiar from the King James Version of the Bible where it is commonly used in the sense of to father (and is repeatedly used in the genealogy ascribed to Jesus in Matthew's gospel: "Abraham begat Isaac; and Isaac begat Jacob; and Jacob begat Judas and his brethren; And Judas begat Phares and Zara of Thamar; and Phares begat Esrom; and Esrom begat Aram…etc., etc." Metaphorically 'begat' means produced, brought forth or similar.

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Many examples of science metaphors are listed in 'Creative comparisons: Making science familiar through language. An illustrative catalogue of figurative comparisons and analogies for science concepts'. Free Download.

polymer backbone modification is like editing

An example of an analogy in science discourse:

"The branding of a research field can be a double-edged sword, Zhukhovitskiy [Dr Alex Zhukhovitskiy, a synthetic polymer chemist from the University of North Carolina at Chapel Hill in the US] acknowledges. 'It can be very distracting if everybody comes up with different ways of naming the same thing.' But the right term can change the perspective from which you think about a problem, he says. 'I think the editing terminology invokes selectivity and precision, in analogy with editing text where you can insert letters, delete them or change their order.' Reframing a research area in this way can also serve as a focal point, concentrating renewed research effort, he adds…

The examples of polymer backbone modification…discovered in the literature included cyclisations, decyclisations, deletions, insertions – and combinations of the above."

James Mitchell Crow (2024) Editing polymer backbones, Chemistry World, February 2024. pp.48-51

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Many examples of science analogies are listed in 'Creative comparisons: Making science familiar through language. An illustrative catalogue of figurative comparisons and analogies for science concepts'. Free Download.

The reference to a double-edge sword is metaphorical, but this metaphor is so widely used it may be considered to be idiomatic.

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cyclic monomers back bite when subjected to ring-opening polymerisation

An example of metaphor in public science discourse:

"In Wooley's lab, her natural product-derived polycarbonates have already demonstrated a propensity for backbone alteration and structural metamorphosis. 'We were finding that when were we were doing ring-opening polymerisation of cyclic monomers, they would back bite and do a rearrangement, essentially,' she says. As a result, the regiochemistry of the monomer insertion into the growing polymer backbone – and the final polymer composition – would shift."

James Mitchell Crow (2024) Editing polymer backbones, Chemistry World, February 2024. pp.48-51

Karen Wooley is Distinguished Professor, Department of Chemistry, Texas A&M University.

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polymers have lifecycles and could be depolymerised at the end of life

An example of an extended metaphor in science journalism:

"The potential implications of this chemistry could be far-reaching. Mastering selective polymer backbone editing could change almost every aspect of the polymer lifecycle – from the way polymers are made to the functionalities they exhibit and to the ways they could be repurposed, upcycled and ultimately depolymerised at end of life."

James Mitchell Crow (2024) Editing polymer backbones, Chemistry World, February 2024. pp.48-51

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species in the polymer kingdom have backbones that can be modified by skeletal editing

An example of the use of extended metaphor in science journalism

"For chemical species in the polymer kingdom, the backbone is their key defining feature. From naming and classification to properties and function, the backbone is central to what makes a polycarbonate a polycarbonate, a polyamide a polyamide, and a polyether a polyether.

A polymer's backbone is the linear string of atoms, arranged in a regular repeating pattern, that forms the core of each polymer chain….

'Polymer backbone editing is an emerging area with a lot of potential to have a big impact,' says Karen Wooley from Texas A&M University in the US. 'People are getting excited about it, bringing in new ideas and it's now just at the precipice, ready to take off and really fly.'…'I love this idea of "Can we later come in and do further backbone modification and skeletal editing?"' Wooley says. 'I think there's a lot of creativity that can be exerted here.' "

James Mitchell Crow (2024) Editing polymer backbones, Chemistry World, February 2024.

Referring to the longest ('core') chain of atoms within a polymer structure as a backbone can be considered an example of metaphor. Here the different types of polymers are considered species (which of itself need not refer to living things) within a kingdom (akin to the kingdoms of animals, fungi, plants, prokaryotes and protists that each have many species of living things).

Skeletal refers to a skeleton, so, arguably (if pedantically), if backbone editing refers to modifications of the longest chain of atoms it should not be seen as synonymous with skeletal editing as that should (by analogy with creatures that have backbones) refer to any modifications in atomic ordering (as the skeleton is not just the backbone in a vertebrate).

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lateral flow urine lipoarabinomannan assay is like a full body biopsy

An example of a simile in science journalism,

"Urine is another sample type that could help reduce the TB diagnostic gap…. This lateral flow urine lipoarabinomannan (LAM) assay is a low-cost point-of-care diagnostic specifically designed to detect active TB in people with HIV. …LAM-based diagnostics are particularly suited for people with HIV because their kidneys tend to be less efficient at filtering the molecule out, meaning there is a higher concentration of LAM in the urine. …

'LAM is a large complex [sugar] molecule that is a component of the TB cell wall,' explains Grant Theron, a TB diagnostics expert at Stellenbosch University in South Africa. The lateral flow tests have polyclonal anti-LAM antibodies that capture LAM shed into urine by the body….

Urine tests are now being explored as a cheap and rapid tool for diagnosing TB in severely ill people without HIV too. A significant advantage of urine tests over those for sputum and tongue swabs is that they can diagnose extrapulmonary TB in addition to pulmonary TB. This is important because around 15% of people with active TB have the disease in organs other than the lungs. 'The urine test is like a full body biopsy,' says Theron."

Nina Notman (2024) Testing times for tuberculosis. Chemistry World, February 2024. pp.44-47

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GeneXpert is the Nespresso machine of the TB tests

An example of a metaphor used in science journalism,

"It was Robert Koch, the German scientist who identified the rod-shaped bacterium Mycobacterium tuberculosis as the cause of TB in 1882…

In recent decades, the WHO [i.e., World Health Organisation] has endorsed some more sensitive diagnostic tools. These include molecular diagnostic tools that look for the DNA of M. tuberculosis in sputum samples. Cepheid's GeneXpert system, endorsed by the WHO in 2010, is the most widely used molecular diagnostic for pulmonary TB. GeneXpert uses cartridges preloaded with reagents. 'It's the Nespresso machine of the TB tests,' [Prof. Madhukar] Pai says. A consortium of collaborators including the Bill & Melinda Gates Foundation and the Foundation for Innovative New Diagnostics (FIND) supported GeneXpert's development. The system processes sputum samples in about 90 minutes, extracting, amplifying and detecting DNA from M. tuberculosis."

Nina Notman (2024) Testing times for tuberculosis. Chemistry World, February 2024.

[Prof. Madhukar Pai is associate director of the International TB Centre at McGill University in Montreal, Canada.]

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water droplets are really chemical dynamos

An example of a metaphor in public science discourse:

"The debate surrounding water microdroplet chemistry is set to continue. Even so, [Stanford University's Professor Richard] Zare remains motivated by his belief that water microdroplets can instigate useful chemical reactions, if not enhance the reactivity and rate of traditional catalysis. Within the last nine months, he and his colleagues have published a significant amount of work in this area. This includes papers reporting that water microdroplets can help turn carbon dioxide and nitrogen into urea; nitrogen into ammonia; benzoic acid into phenol; and toluene into phenylacetic acid.

'Normal water, you think puts out fire and is supposedly benign and inert, but I'm telling you water droplets at their surface are really chemical dynamos,' Zare concludes."

Rebecca Trager, Are water microdroplets really chemical dynamos?, Chemistry World, February 2024, pp.38-40

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sodium borohydride is modern lemon juice

An example of a metaphor in science journalism,

"[Stanford University's Professor Richard] Zare's team made its hydrogen peroxide discovery while trying to synthesise gold nanostructures in microdroplets, armed with the knowledge that Michael Faraday had made gold films with lemon juice. They added sodium borohydride – which Zare calls 'modern lemon juice' – to water microdroplets and found that the reaction occurred 100,000 times faster than in bulk liquid."

Rebecca Trager, Are water microdroplets really chemical dynamos?, Chemistry World, February 2024, pp.38-40

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atoms and ions are more like gas giant planets than billiard balls

An example of a teaching analogy:

"The materials used to make the macroscopic models do not reflect the world at the molecular scale. Pieces that represent ions or atoms are bits of plastic or wood that have distinct surfaces and definitive volumes – but ions and atoms do not: they are fuzzy objects more like gas giant planets with their atmospheres slowly thinning out with altitude than ball bearings or marbles or snooker/ billiard balls.

[This atmospheric analogy seems a good comparison (positive analogy) in terms of the nature of the transition – there is no physical 'end' of the earth's atmosphere. However (negative analogy), in terms of scaling, the earth's atmospheric density drops off relatively more quickly than electron density around an atom. (That is, positing a nominal 'top of the atmosphere' is a better approximation, for a planet than positing an 'edge of the orbital' for an atomic electron.) The atmosphere is made up of a vast number of molecules each of which can reach escape velocity (due to the various interactions that can lead to a molecule being on the tail of the Maxwell-Boltzmann distribution) and potentially leave the atmosphere individually, whereas an orbital contains at most two electrons which can only leave if given a sufficient quantum of energy to completely shift elsewhere.]"
Taber, Keith S. (2024) Chemical pedagogy. Instructional approaches and teaching techniques in chemistry. Royal Society of Chemistry.

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Taber, Keith S. (2024) Chemical pedagogy. Instructional approaches and teaching techniques in chemistry. Royal Society of Chemistry. [Download Chapter 1]