Substantia <p style="text-align: justify;"><em>Substantia</em> is a peer-reviewed academic international journal dedicated to the history and philosophy of Chemistry and edited by the University of Florence. Topics of interest include traditional and innovative perspectives in the development of Chemistry. Fundamentals and implications of chemical theories and related sciences, interdisciplinary works (highlighting the interconnections between Chemistry, other scientific disciplines, arts, technology, social and human sciences), contributions from unpublished sources are welcome. The journal is published open access and offers top quality original full papers, essays, experimental works, reviews, biographies and dissemination manuscripts. All contributions are in English.</p> en-US <ul> <li class="show">Copyright on any open access article in Substantia published by FUP is retained by the author(s).</li> <li class="show">Authors grant FUP a license to publish the article and identify itself as the original publisher.</li> <li class="show">Authors also grant any third party the right to use the article freely as long as its integrity is maintained and its original authors, citation details and publisher are identified.</li> <li class="show">The <a class="is-external" href="" target="_blank" rel="noopener">Creative Commons Attribution License 4.0</a> formalizes these and other terms and conditions of publishing articles.</li> <li class="show">In accordance with our Open Data policy, the <a class="is-external" href="" target="_blank" rel="noopener">Creative Commons CC0 1.0 Public Domain Dedication waiver</a> applies to all published data in Substantia open access articles.</li> </ul> <h4 style="text-align: left;">&nbsp;</h4> (Pierandrea Lo Nostro) (Alessandro Pierno, Firenze University Press) Sun, 31 Mar 2019 00:00:00 +0000 OJS 60 I won a project! Juan Manuel García Ruiz ##submission.copyrightStatement## Sun, 31 Mar 2019 00:00:00 +0000 Similarities and contrasts in the structure and function of the calcium transporter ATP2A1 and the copper transporter ATP7B <p class="p1">Ca<sup>2+</sup> and Cu<sup>2+</sup> ATPases are enzyme proteins that utilize ATP for active transport of Ca<sup>2+</sup> or Cu<sup>2+</sup> across intracellular or cellular membranes.<sup>1-4</sup> These enzymes are referred to as P-type ATPases since they utilize ATP through formation of a phosphorylated intermediate (E-P) whose phosphorylation potential affects orientation and affinity of bound cations by means of extended conformational changes. Thereby specific cations are transported across membranes, forming transmembrane gradients in the case of Ca<sup>2+</sup>, or accepting Cu<sup>2+</sup> from delivering proteins on one side of the membrane and releasing it to carrier proteins on the other side. Binding of Ca<sup>2+</sup> or Cu<sup>2+</sup> is required for enzyme activation and utilization of ATP by transfer of ATP terminal phosphate to a conserved aspartate residue. The ATPase protein is composed of a transmembrane region composed of helical segments and including the cation binding site (TMBS), and a cytosolic headpiece with three domains (A, N and P) containing the catalytic and phosphorylation site. The number of helical segments and the cytosolic headpieces present significant differences in the two enzymes. In addition, details of transmembrane cation extrusion are different. The Ca<sup>2+</sup> and Cu<sup>2+</sup> ATPase sustain vital physiological functions, such as muscle contraction and relaxation, activation of several cellular enzymes, and elimination of excess cation concentrations. A historic review of studies on chemical and physiological mechanisms of the Ca<sup>2+</sup> and Cu<sup>2+</sup> ATPase is presented.</p> Giuseppe Inesi ##submission.copyrightStatement## Tue, 02 Oct 2018 00:00:00 +0000 Finding Na,K-ATPase II - From fluxes to ion movements <p class="p1">After identification of the Na,K-ATPase as active ion transporter that maintains the Na<sup>+</sup> and K<sup>+</sup> concentration gradient across the membrane of virtually all animal cells, a long history of mechanistic studies began in which enzyme activity and ion-transport were intensively investigated. A basis for detailed understanding was laid in the so-called Post-Albers pump cycle. Developing new experimental techniques allowed the determination of different flux modes, the analysis of the kinetics of enzyme phosphorylation and dephosphorylation as well as of the transport of Na<sup>+</sup> and K<sup>+</sup> ions across the membrane. The accumulation of results from transport studies allowed the proposal of the gated channel concept that turned out to be a successful approach to explain the transport-related experimental findings. Eventually, it found its counterpart in the high-resolution structure of the ion pump. Recently it turned out that simple mutations of the Na,K-ATPase are the cause of several diseases.</p> Hans-Jürgen Apell ##submission.copyrightStatement## Sun, 31 Mar 2019 00:00:00 +0000 Range separation: the divide between local structures and field theories <p class="p1">This work presents parallel histories of the development of two modern theories of condensed matter: the theory of electron structure in quantum mechanics, and the theory of liquid structure in statistical mechanics. Comparison shows that key revelations in both are not only remarkably similar, but even follow along a common thread of controversy that marks progress from antiquity through to the present. This theme appears as a creative tension between two competing philosophies, that of short range structure (atomistic models) on the one hand, and long range structure (continuum or density functional models) on the other. The timeline and technical content are designed to build up a set of key relations as guideposts for using density functional theories together with atomistic simulation.</p> David M. Rogers ##submission.copyrightStatement## Sun, 31 Mar 2019 00:00:00 +0000 Hydration of silica and its role in the formation of quartz veins - Part 2 <p class="p1">The aqueous chemistry of silica and the formation of abundant polymeric silica species in natural sediment accumulations is set out in Part 1. Part 2 continues to describe the amorphous silica in sediments and presents more evidence for the formation of quartz veins from silica gels. The physical chemistry for the formation of oolites in quartz veins, ptygmatic folding of quartz veins, the enhanced growth of crystals in quartz veins, the precipitation of gold in quartz and the mechanism for replacement or metasomatism by quartz (silicification) are detailed. Current physical chemistry applies not only to precursor silica gel but also to the hydrous precursors of other crystalline rock minerals such as clays, mica, hydrous ferromagnesian minerals and mineral deposits. “The Origin of Rocks and Mineral Deposits - using current physical chemistry of small particle systems” provides a new basis for understanding geological phenomena. This has now been published in Elliston<sup>1</sup> 2017 (Connor Court, Brisbane, ISBN 978-1-925501-36-0).</p> John Elliston ##submission.copyrightStatement## Sun, 31 Mar 2019 00:00:00 +0000 Chuckles and Wacky Ideas <p class="p1">Another big group of dolphins had just surfaced alongside our moving vessel —leaping and splashing and calling mysteriously back and forth in their squeally, whistly way, with many babies swift alongside their mothers. And this time, confined to just the surface of such deep and lovely lives, I was becoming unsatisfied. I wanted to know what they were experiencing, and why to us they feel so compelling and so—close. This time I allowed myself to ask them the question that for a scientist is forbidden fruit: Who are you? Scientists usually steer firmly from questions about the inner lives of animals. Surely they have inner lives of some sort. But like a child who is admonished that what they really want to ask is impolite, a young scientist is taught that the animal mind—if there is such—is unknowable. Permissible questions are “it” questions: about where it lives, what it eats, what it does when danger threatens, how it breeds. But always forbidden—always forbidden—is the one question that might open the door to the interior: Who? There are good reasons to avoid so fraught an inquiry and the cans of worms such a door could open. But the barrier between humans and animals is artificial, because humans are animals. And now, watching these dolphins, I was tired of being so artificially polite; I wanted more intimacy. I felt time slipping for both of us, and I did not want to risk having to say good-bye and realizing that I’d never really said hello. During the cruise I’d been reading about elephants, and elephant minds were on my own mind as I wondered about the dolphins and watched them pacing fluidly and freely in their ocean realm. When a poacher kills an elephant, he doesn’t just kill the elephant who dies. The family may lose the crucial memory of their elder matriarch, who knew where to travel during the very toughest years of drought to reach the food and water that would allow them to continue living. Thus one bullet may, years later, bring more deaths. Watching dolphins while thinking of elephants, what I realized is: when others recognize and depend on certain individuals, when a death makes the difference for individuals who survive, when relationships define us, we have traveled across a certain blurry boundary in the history of life on Earth—“it” has become “who.” “Who” animals know who they are; they know who their family and friends are. They know their enemies. They make strategic alliances and cope with chronic rivalries. They aspire to higher rank and wait for their chance to challenge the existing order. Their status affects their offspring’s prospects. Their life follows the arc of a career. Personal relationships define them. Sound familiar? Of course. “They” includes us. But a vivid, familiar life is not the domain of humans alone. We look at the world through our own eyes, naturally. But by looking from the inside out, we see an inside-out world. This book takes the perspective of the world outside us—a world in which humans are not the measure of all things, a human race among other races. To understand anything, really, one must go deep, to the roots. In our estrangement from nature we have severed our sense of the community of life and lost touch with the experience of other animals. So while I went in search of particular “who” animals, I delved into new findings about thought, emotion, and consciousness that apply to many animals. And because everything about life occurs along a sliding scale, understanding the human animal becomes easier in context, seeing our human thread woven into the living web among the strands of so many others. This project differs from other “animal thinking” books in one fundamental way. I’d intended to take a bit of a break from my usual writing about conservation issues, to circle back to my first love: simply seeing what animals do, and asking why they do it. I traveled to observe some of the most protected creatures in the world—elephants of Amboseli in Kenya, wolves of Yellowstone in the United States, and killer whales in the waters of the Pacific Northwest—yet in each place I found the animals feeling human pressures that directly affect what they do, where they go, how long they live, and how their families fare. So in this book we encounter the minds of other animals and we listen—to what they need us to hear. The story that tells itself is not just what’s at stake but who is at stake. The greatest realization is that all life is one. I was seven years old when my father and I fixed up a small shed in our Brooklyn yard and got some homing pigeons. Watching how they built nests in their cubbyholes, seeing them courting, arguing, caring for their babies, flying off and faithfully returning, how they needed food, water, a home, and one another, I realized that they lived in their apartments just as we lived in ours. Just like us, but in a different way. Over my lifetime, living with, studying, and working with many other animals in their world and ours has only broadened and deepened —and reaffirmed—my impression of our shared life. That’s the impression I’ll endeavor to share with you in the pages that follow.</p> Carl Safina ##submission.copyrightStatement## Sun, 31 Mar 2019 00:00:00 +0000 The increased anthropogenic gas emissions in the atmosphere and the rising of the Earth’s temperature: are there actions to mitigate the global warming? <p>Some frozen bodies have been recently discovered in the Alp glaciers because the global warming is forcing the ice to retreat. Many years have passed since the first perception of a strong link between the temperature of the Earth and the amount of some gases in the atmosphere, the so called greenhouse gases. Today there is a general consensus among the governments, the scientists and industrial organizations of most countries in recognizing the relationship between the increase of the atmospheric CO<sub>2</sub> concentration resulting from over a century of combustion of fossil fuels and the observed global warming. The development of technologies to reduce the anthropogenic emissions should not be further delayed, in accordance with the Paris Agreement that recommended keeping the global mean temperature well below 2 °C above pre-industrial levels to reduce the risks and impacts of climate change.</p> <p>This paper gives an overview of the different greenhouse gases, their emissions by economic sectors and the international treaties that require the most developed countries to pursue the objective of reducing their greenhouse gas emissions. Amongst the different actions directed towards a low-carbon economy, the chemical capture of CO<sub>2 </sub>from large stationary emission points is the most efficient and widespread option. Additionally, new technologies are currently exploited to capture CO<sub>2</sub> directly from air and to convert CO<sub>2</sub> into fuels and valuable chemicals.</p> Francesco Barzagli, Fabrizio Mani ##submission.copyrightStatement## Sun, 31 Mar 2019 00:00:00 +0000 The ‘Consciousness-Brain’ relationship <p class="p1">From a thought experiment on the observation of a human intellect by itself, we will attempt to demonstrate that, unlike what many neuroscientists postulate, assemblies of neurons do not generate consciousness: Consciousness pre-exists any material system.</p> Jean Pierre Gerbaulet, Marc Henry ##submission.copyrightStatement## Sun, 31 Mar 2019 00:00:00 +0000 Dmitry I. Mendeleev and his time <p class="p1">The history of the creation of Periodic table and of the Mendeleev’s discovery of Periodic Law is considered. The different approaches used by Mendeleev’s colleagues are discussed. The contribution of the Periodic system to the extension of the scientific ideas in geology and best of all in geochemistry and mineralogy is illustrated by the discovery of new chemical elements and by the isomorphic replacements in minerals. The details of uneasy history of Mendeleev’s nomination to the St. Petersburg Academy and for the Nobel Prize are given.</p> Dmitry Pushcharovsky ##submission.copyrightStatement## Sun, 31 Mar 2019 00:00:00 +0000 Early contributions of crystallography to the atomic theory of matter <p class="p1">After briefly presenting early hypotheses on the submicroscopic origin of symmetry and polyhedral morphology in the crystals, the structural model proposed by Haüy in 1784, based on the periodic repetition of integrant molecules made up of simple molecules, is discussed. It is then highlighted how – through investigation of crystal hemihedry, isomorphism (mixed crystals) and optical activity – researches aiming at overtaking drawbacks of Haüy’s model brought basic ideas to achieve the modern knowledge of the atomic structure of matter. The atomic-scale interpretation of properties of the crystalline state soundly contributed, among others, to properly define molecules and atoms, determine the atomic weights, hypothesize stereoisomerism, build the periodic table of elements and define ionic radii and bond.</p> Giovanni Ferraris ##submission.copyrightStatement## Sun, 31 Mar 2019 00:00:00 +0000 Bringing Together Academic and Industrial Chemistry: Edmund Ronalds’ Contribution <p class="p1">Born 200 years ago, Edmund Ronalds (1819–1889) obtained his doctorate in Germany under Liebig, became a professor at Queen’s College Galway and ran the little-studied but significant Bonnington Chemical Works in Edinburgh. His few mentions in the modern literature relate generally to the legacies of his actual and assumed academic supervisors of renown, yet his hitherto unknown mentors included family members and the important chemists Graham, Magnus, Tennant and Tennent. The novelty of his shift from university to manufacture has also been noted. With the aid of little-known primary sources, this biography details the evolution of Ronalds’ career, exploring the context and influences for his diverse accomplishments and in particular the new and successful ways he bridged academia and industry through technological education and industrial research.</p> Beverley F. Ronalds ##submission.copyrightStatement## Sun, 31 Mar 2019 00:00:00 +0000