WikiJournal of Science
WikiJournal of Science
Open access • Publication charge free • Public peer review • Wikipedia-integrated
VOLUME 2 (2019)
ISSUE 1
Previous issue
Author: Collin Knopp-Schwyn
Widgiemoolthalite is a rare hydrated nickel(II) carbonate mineral with the chemical formula (Ni,Mg)5(CO3)4(OH)2·5H2O. Usually bluish-green in color, it is a brittle mineral formed during the weathering of nickel sulfide. Present on gaspéite surfaces, widgiemoolthalite has a Mohs scale hardness of 3.5 and an unknown though likely disordered crystal structure. Widgiemoolthalite was first discovered in 1992 in Widgiemooltha, Western Australia, which was its only known source as of 2016. It was named in 1993 by the three researchers who first reported its existence, Ernest H. Nickel, Bruce W. Robinson, and William G. Mumme.
doi: 10.15347/WJS/2019.007
Author: Ignacio Lopez de Blas
Lysenin is a pore-forming toxin present in the coelomic fluid of the earthworm Eisenia fetida. Pore-forming toxins (PFTs) are proteinaceous virulence factors produced by many pathogenic bacteria. Following the general mechanism of action of PFTs, lysenin is secreted as a soluble monomer that binds specifically to the membrane receptor sphingomyelin. After attachment, lysenin forms a 9-copy oligomer (nonamer) prepore on the lipid bilayer before membrane insertion. The biological role of lysenin is still unclear, however the most plausible theory is that it is part of an immune-avoiding mechanism. There are many proposed technological applications proposed for lysenin, and understanding its molecular role in bacterial infection could help in developing different antibiotic strategies to solve the problem of multiple drug resistance in bacteria.
doi: 10.15347/WJS/2019.006
Author: Anthony Lin
In computer science, binary search, also known as half-interval search, logarithmic search, or binary chop, is a search algorithm that finds a position of a target value within a sorted array. Binary search compares the target value to an element in the middle of the array. If they are not equal, the half in which the target cannot lie is eliminated and the search continues on the remaining half, again taking the middle element to compare to the target value, and repeating this until the target value is found. If the search ends with the remaining half being empty, the target is not in the array. [...] Binary search runs in logarithmic time in the worst case, making comparisons, where is the number of elements in the array, the is Big O notation, and is the logarithm. Binary search is faster than linear search except for small arrays. However, the array must be sorted first to be able to apply binary search. There are specialized data structures designed for fast searching, such as hash tables, that can be searched more efficiently than binary search. However, binary search can be used to solve a wider range of problems, such as finding the next-smallest or next-largest element in the array relative to the target even if it is absent from the array. There are numerous variations of binary search. In particular, fractional cascading speeds up binary searches for the same value in multiple arrays. Fractional cascading efficiently solves a number of search problems in computational geometry and in numerous other fields. Exponential search extends binary search to unbounded lists. The binary search tree and B-tree data structures are based on binary search. doi: 10.15347/WJS/2019.005
Authors: Michael J Stear, David Piedrafita, Caitlin J Jenvey, Sarah Sloan, Dalal Alenizi, Callum Cairns
One of the most important parasites of sheep and goats is the nematode Teladorsagia circumcincta. This is common in cool, temperate areas. There is considerable variation among lambs and kids in susceptibility to infection. Much of the variation is genetic and influences the immune response. The parasite induces a type I hypersensitivy response which is responsible for the relative protein deficiency which is characteristic of severely infected animals. There are mechanistic mathematical models which can predict the course of infection. There are a variety of ways to control the infection and a combination of control measures is likely to provide the most effective and sustainable control.
doi: 10.15347/WJS/2019.004
Author: Michael Bech
Baryonyx (/ˌbæriˈɒnɪks/) is a genus of theropod dinosaur which lived in the Barremian stage of the Early Cretaceous Period, about 130–125 million years ago. The first skeleton was discovered in 1983 in the Weald Clay Formation of Surrey, England, and became the holotype specimen of B. walkeri, named by palaeontologists Alan J. Charig and Angela C. Milner in 1986. The generic name, Baryonyx, means "heavy claw" and alludes to the animal's very large claw on the first finger; the specific name, walkeri, refers to its discoverer, amateur fossil collector William J. Walker. The holotype specimen is one of the most complete theropod skeletons from the UK (and remains the most complete spinosaurid), and its discovery attracted media attention. Specimens later discovered in other parts of the United Kingdom and Iberia have also been assigned to the genus. doi: 10.15347/WJS/2019.003
Author: Mike Christie
Ice drilling allows scientists studying glaciers and ice sheets to gain access to what is beneath the ice, to take measurements along the interior of the ice, and to retrieve samples. Instruments can be placed in the drilled holes to record temperature, pressure, speed, direction of movement, and for other scientific research, such as neutrino detection. [...] Many different methods have been used since 1840, when the first scientific ice drilling expedition attempted to drill through the Unteraargletscher in the Alps. Two early methods were percussion, in which the ice is fractured and pulverized, and rotary drilling, a method often used in mineral exploration for rock drilling. In the 1940s, thermal drills began to be used; these drills melt the ice by heating the drill. Drills that use jets of hot water or steam to bore through ice soon followed. A growing interest in ice cores, used for palaeoclimatological research, led to ice coring drills being developed in the 1950s and 1960s, and there are now many different coring drills in use. For obtaining ice cores from deep holes, most investigators use cable-suspended electromechanical drills, which use an armoured cable to carry electrical power to a mechanical drill at the bottom of the borehole. In 1966, a US team successfully drilled through the Greenland ice sheet at Camp Century, at a depth of 1,387 metres (4,551 ft). Since then many other groups have succeeded in reaching bedrock through the two largest ice sheets, in Greenland and Antarctica. Recent projects have focused on finding drilling locations that will give scientists access to very old undisturbed ice at the bottom of the borehole, since an undisturbed stratigraphic sequence is required to accurately date the information obtained from the ice. doi: 10.15347/WJS/2019.002
Author: Natalie A Borg
RIG-I (retinoic-acid inducible gene I, also known as DDX58) is the best characterized receptor within the RIG-I like receptor (RLR) family. Together with MDA5 (melanoma differentiation-associated 5) and LGP2 (laboratory of genetics and physiology 2), this family of cytoplasmic pattern recognition receptors (PRRs) are sentinels for intracellular viral RNA that is a product of viral infection. The RLR receptors provide frontline defence against viral infections in most tissues.
doi: 10.15347/WJS/2019.001
VOLUME 1 (2018)
ISSUE 2
Previous issue
Author: Andrew Z Colvin
Peripatric speciation is a mode of speciation in which a new species is formed from an isolated peripheral population. Since peripatric speciation resembles allopatric speciation, in that populations are isolated and prevented from exchanging genes, it can often be difficult to distinguish between them. Nevertheless, the primary characteristic of peripatric speciation proposes that one of the populations is much smaller than the other. The terms peripatric and peripatry are often used in biogeography, referring to organisms whose ranges are closely adjacent but do not overlap, being separated where these organisms do not occur—for example on an oceanic island compared to the mainland. Such organisms are usually closely related (e.g. sister species); their distribution being the result of peripatric speciation. [...] The concept of peripatric speciation was first outlined by the evolutionary biologist Ernst Mayr in 1954. Since then, other alternative models have been developed such as centrifugal speciation, that posits that a species' population experiences periods of geographic range expansion followed by shrinking periods, leaving behind small isolated populations on the periphery of the main population. Other models have involved the effects of sexual selection on limited population sizes. Other related models of peripherally isolated populations based on chromosomal rearrangements have been developed such as budding speciation and quantum speciation. The existence of peripatric speciation is supported by observational evidence and laboratory experiments. Scientists observing the patterns of a species biogeographic distribution and its phylogenetic relationships are able to reconstruct the historical process by which they diverged. Further, oceanic islands are often the subject of peripatric speciation research due to their isolated habitats—with the Hawaiian Islands widely represented in much of the scientific literature. doi: 10.15347/WJS/2018.008
Author: Mikhail Boldyrev
Lead is a chemical element with the atomic number 82 and the symbol Pb (from the Latin plumbum). It is a heavy metal that is denser than most common materials. Lead is soft and malleable, and has a relatively low melting point. When freshly cut, lead is silvery with a hint of blue; it tarnishes to a dull gray color when exposed to air. Lead has the highest atomic number of any stable element and concludes three major decay chains of heavier elements. [...] Lead is a relatively unreactive post-transition metal. Its weak metallic character is illustrated by its amphoteric nature; lead and its oxides react with acids and bases, and it tends to form covalent bonds. Compounds of lead are usually found in the +2 oxidation state rather than the +4 state common with lighter members of the carbon group. Exceptions are mostly limited to organolead compounds. Like the lighter members of the group, lead tends to bond with itself; it can form chains, rings and polyhedral structures. Lead is easily extracted from its ores; prehistoric people in Western Asia knew of it. Galena, a principal ore of lead, often bears silver, interest in which helped initiate widespread extraction and use of lead in ancient Rome. Lead production declined after the fall of Rome and did not reach comparable levels until the Industrial Revolution. In 2014, annual global production of lead was about ten million tonnes, over half of which was from recycling. Lead's high density, low melting point, ductility, and relative inertness to oxidation make it useful. These properties, combined with its relative abundance and low cost, resulted in its extensive use in construction, plumbing, batteries, bullets and shot, weights, solders, pewters, fusible alloys, white paints, leaded gasoline, and radiation shielding. In the late 19th century, lead's toxicity was recognized, and its use has since been phased out of many applications. Lead is a toxin that accumulates in soft tissues and bones, it acts as a neurotoxin damaging the nervous system and interferences with the function of biological enzymes. It is particularly problematic in children: even if blood levels are promptly normalized with treatment, neurological disorders, such as brain damage and behavioral problems, may result. doi: 10.15347/WJS/2018.007
VOLUME 1 (2018)
ISSUE 1
Previous issue
Author: Mike Christie
Radiocarbon dating (also referred to as carbon dating or carbon-14 dating) is a method for determining the age of an object containing organic material by using the properties of radiocarbon, a radioactive isotope of carbon. [...] The method was developed in the late 1940s by Willard Libby, who received the Nobel Prize in Chemistry for his work in 1960. It is based on the fact that radiocarbon (14 C) is constantly being created in the atmosphere by the interaction of cosmic rays with atmospheric nitrogen. The resulting 14 C combines with atmospheric oxygen to form radioactive carbon dioxide, which is incorporated into plants by photosynthesis; animals then acquire 14 C by eating the plants. When the animal or plant dies, it stops exchanging carbon with its environment, and from that point onwards the amount of 14 C it contains begins to decrease as the 14 C undergoes radioactive decay. Measuring the amount of 14 C in a sample from a dead plant or animal such as a piece of wood or a fragment of bone provides information that can be used to calculate when the animal or plant died. The older a sample is, the less 14 C there is to be detected, and because the half-life of 14 C is about 5,730 years, the oldest dates that can be reliably measured by this process date to around 50,000 years ago, although special preparation methods occasionally permit accurate analysis of older samples. Research has been ongoing since the 1960s to determine what the proportion of 14 C in the atmosphere has been over the past fifty thousand years. The resulting data, in the form of a calibration curve, is now used to convert a given measurement of radiocarbon in a sample into an estimate of the sample's calendar age. Other corrections must be made to account for the proportion of 14 C in different types of organisms (fractionation), and the varying levels of 14 C throughout the biosphere (reservoir effects). Additional complications come from the burning of fossil fuels such as coal and oil, and from the above-ground nuclear tests done in the 1950s and 1960s. Because the time it takes to convert biological materials to fossil fuels is substantially longer than the time it takes for its 14 C to decay below detectable levels, fossil fuels contain almost no 14 C, and as a result there was a noticeable drop in the proportion of 14 C in the atmosphere beginning in the late 19th century. Conversely, nuclear testing increased the amount of 14 C in the atmosphere, which attained a maximum in about 1965 of almost twice what it had been before the testing began. Measurement of radiocarbon was originally done by beta-counting devices, which counted the amount of beta radiation emitted by decaying 14 C atoms in a sample. Accelerator mass spectrometry (AMS) has since become the method of choice; it counts 14 C atoms in the sample directly, rather than just the few that happen to decay during the measurements; it can therefore be used with much smaller samples (as small as individual plant seeds), and gives results much more quickly. The development of radiocarbon dating has had a profound impact on archaeology: in addition to permitting more accurate dating within archaeological sites than previous methods, it allows comparison of dates of events across great distances, and it has allowed key transitions in prehistory to be dated, such as the end of the last ice age. doi: 10.15347/WJS/2018.006
Authors: Guy Vandegrift, A card game for Bell's theorem and its loopholes
In 1964 John Stewart Bell made an observation about the behavior of particles separated by macroscopic distances that had puzzled physicists for at least 29 years, when Einstein, Podolsky and Rosen put forth the famous EPR paradox. Bell made certain assumptions leading to an inequality that entangled particles are routinely observed to violate in what are now called Bell test experiments. As an alternative to showing students a "proof" of Bell's inequality, we introduce a card game that is impossible to win. The solitaire version is so simple it can be used to introduce binomial statistics without mentioning physics or Bell's theorem. Things get interesting in the partners' version of the game because Alice and Bob can win, but only if they cheat. We have identified three cheats, and each corresponds to a Bell's theorem "loophole". This gives the instructor an excuse to discuss detector error, causality, and why there is a maximum speed at which information can travel.
doi: 10.15347/WJS/2018.005
Authors: Tatiana P. Soares da Costa, Cody J. Hall
Amino acids are an essential building block of all life and are commonly incorporated into extending polypeptide chains to produce proteins. Lysine is one such amino acid and is classified as basic and positively charged at physiological pH due to the presence of an additional amino chemical group on the side chain. Lysine has two main biosynthetic pathways, namely the diaminopimelate and α-aminoadipate pathways, which employ different enzymes and substrates and are found in different organisms. Lysine catabolism occurs through one of several pathways, the most common of which is the saccharopine pathway. Lysine plays several roles in humans, most importantly proteinogenesis, but also in the crosslinking of collagen polypeptides, uptake of essential mineral nutrients, and in the production of carnitine, which is key in fatty acid metabolism. Furthermore, lysine is often involved in histone modifications, and thus, impacts the epigenome. Due to the importance of lysine in several biological processes, a lack of lysine can lead to several disease states including; defective connective tissues, impaired fatty acid metabolism, anaemia, and systemic protein-energy deficiency. In juxtaposition to this, an overabundance of lysine, caused by ineffective catabolism, can cause severe neurological issues.
doi: 10.15347/WJS/2018.004
Authors: Shih Chieh Chang, Saumya Bajaj, George Chandy
Stichodactyla toxin (ShK) is a 35-residue basic peptide from the sea anemone Stichodactyla helianthus that blocks a number of potassium channels. An analogue of ShK called ShK-186 or Dalazatide is in human trials as a therapeutic for autoimmune diseases.
doi: 10.15347/WJS/2018.003
Author: Boris Tsirelson
While modern mathematics use many types of spaces, such as Euclidean spaces, linear spaces, topological spaces, Hilbert spaces, or probability spaces, it does not define the notion of "space" itself. [...] A space consists of selected mathematical objects that are treated as points, and selected relationships between these points. The nature of the points can vary widely: for example, the points can be elements of a set, functions on another space, or subspaces of another space. It is the relationships that define the nature of the space. More precisely, isomorphic spaces are considered identical, where an isomorphism between two spaces is a one-to-one correspondence between their points that preserves the relationships. For example, the relationships between the points of a three-dimensional Euclidean space are uniquely determined by Euclid's axioms, and all three-dimensional Euclidean spaces are considered identical. Topological notions such as continuity have natural definitions in every Euclidean space. However, topology does not distinguish straight lines from curved lines, and the relation between Euclidean and topological spaces is thus "forgetful". Relations of this kind are sketched in Figure 1, and treated in more detail in the Section "Types of spaces". It is not always clear whether a given mathematical object should be considered as a geometric "space", or an algebraic "structure". A general definition of "structure", proposed by Bourbaki, embraces all common types of spaces, provides a general definition of isomorphism, and justifies the transfer of properties between isomorphic structures. doi: 10.15347/WJS/2018.002 Editorial | The aims and scope of WikiJournal of Science
Authors: Thomas Shafee, WikiJournal of Science editorial board
WikiJournal of Science is an open access, peer reviewed journal, free of publication charges for its authors. It has Wikipedia-integration as a key feature and aims to encourage and recognise contributions to Wikipedia by academics. It is a sister journal to the established WikiJournal of Medicine, and covers science, technology, engineering and mathematics. This editorial will discuss the current aims and future scope of the journal, as well as the WikiJournal format in general.
doi: 10.15347/WJS/2018.001
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