Outreach Testing of Ancient Astronomy

This work is an outreach approach to an ubiquitous recent problem in secondary-school education: how to face back the decreasing interest in natural sciences shown by students under ‘pressure’ of convenient resources in digital devices/applications. The approach rests on two features. First, empowering of teen-age students to understand regular natural events around, as very few educated people they meet could do. Secondly, an understanding that rests on personal capability to test and verify experimental results from the oldest science, astronomy, with simple instruments as used from antiquity down to the Renaissance (a capability restricted to just solar and lunar motions). Because lengths in astronomy and daily life are so disparate, astronomy basically involved observing and registering values of angles (along with times), measurements being of two types, of angles on the ground and of angles in space, from the ground. First, the gnomon, a simple vertical stick introduced in Babylonia and Egypt, and then in Greece, is used to understand solar motion. The gnomon shadow turns around during any given day, varying in length and thus angle between solar ray and vertical as it turns, going through a minimum (noon time, at a meridian direction) while sweeping some angular range from sunrise to sunset. Further, the shadow minimum length varies through the year, with times when shortest and sun closest to vertical, at summer solstice, and times when longest, at winter solstice six months later. The extreme directions at sunset and sunrise correspond to the solstices, swept angular range greatest at summer, over 180 degrees, and the opposite at winter, with less daytime hours; in between, spring and fall equinoxes occur, marked by collinear shadow directions at sunrise and sunset. The gnomon allows students to determine, in addition to latitude (about 40.4° North at Madrid, say), the inclination of earth equator to plane of its orbit around the sun (ecliptic), this fundamental quantity being given by half the difference between solar distances to vertical at winter and summer solstices, with value about 23.5°. Day and year periods greatly differing by about 2 ½ orders of magnitude, 1 day against 365 days, helps students to correctly visualize and interpret the experimental measurements. Since the gnomon serves to observe at night the moon shadow too, students can also determine the inclination of the lunar orbital plane, as about 5 degrees away from the ecliptic, thus explaining why eclipses are infrequent. Independently, earth taking longer between spring and fall equinoxes than from fall to spring (the solar anomaly), as again verified by the students, was explained in ancient Greek science, which posited orbits universally as circles or their combination, by introducing the eccentric circle, with earth placed some distance away from the orbital centre when considering the relative motion of the sun, which would be closer to the earth in winter. In a sense, this can be seen as hint and approximation of the elliptic orbit proposed by Kepler many centuries later.

El tiempo como sustancia de la forma : una aproximación al Museo de Arte Romano de Mérida desde los presupuestos del vitalismo

El modelo dominante durante la Era Moderna asume la presencia del hombre como sujeto dentro del gran engranaje mecánico del Cosmos. Asimismo, recoge una idea acerca del ser natural dentro de la tradición ontológica iniciada por el eleatismo presocrático que concibe a éste como lo inmutable y estático frente al cambio y al movimiento, los cuales se constituyen como meras apariencias. Durante el periodo anterior a la aparición de los grandes filósofos griegos se produce una transformación en donde, de la inicial cosmología vinculada a un tiempo primordial, se pasará a una visión del Universo como ente indestructible, atemporal, inmutable, perfecto, geométrico y espacial. Si en Demócrito se admite un universo sometido al azar y a la necesidad, en Platón el Universo sólo atiende a la necesidad. Este modelo ontológico se pone en entredicho cuando el hombre ya no es concebido como pieza de un sistema más amplio, sino como centro radical del pensamiento. La condición radical del hombre es entonces su propia vida, siendo éste el concepto troncal del denominado vitalismo cuyo más influyente representante en España es José Ortega y Gasset. El estatismo del ser –del hombre- pierde sentido; en palabras del propio Ortega, “no es un ser sino un estar siendo” lo que caracteriza a la vida humana. La razón cartesiana es ahora la razón vital y su objeto de estudio no es la naturaleza sino el propio devenir, es decir, el tiempo, la historia. Este planteamiento es fundamental para comprender el edificio que es objeto de este estudio, el Museo de Arte Romano de Mérida (1980-1985) de Rafael Moneo. Por ello el concepto de tiempo es utilizado como marco y estructura de la presente tesis, a sabiendas del notorio y muy significativo papel que este edificio desempeñó en la carrera de su autor y en el panorama nacional e internacional de la arquitectura y de la museología. Este proyecto nos permite acercarnos al pensamiento de su autor a través de un edificio que, aun habiendo sido ampliamente reconocido, no cuenta con un estudio suficientemente exhaustivo que recoja la amplitud y riqueza que encierra. Esta tesis no es un compendio de lo que ya se ha investigado sobre Mérida; es una aproximación global e interpretativa cuyo sentido sólo puede concebirse al vislumbrar la estructura completa de la misma en sintonía con el "lógos" vital, histórico y narrativo que el proyecto encierra. Se revisará la concepción histórica según la cual, la configuración espacial de la forma habría tenido primacía respecto a su configuración temporal, al remitir esta última a una condición espacializada y circunstancial. La componente vicaria de la circunstancia será elevada por Ortega a la categoría de esencial, visualizando así una paradoja cuya reformulación nos lleva a la concepción de un tiempo sustancial. El diccionario de la RAE, en su tercera acepción, define la sustancia como “aquello que permanece en algo que cambia”, lo cual nos remite al pensamiento antiguo. Se mostrará que lo que permanece no necesariamente implica una concepción estática y eleática de la forma, que la arquitectura esencial no es unívocamente la arquitectura atemporal del platonismo y que cabe concebir la "firmitas" desde la atención a la "durée" bergsoniana. Al asociar tradicionalmente la sustancia con el referido estatismo, se margina al tiempo y a la duración a lo no sustancial; por ello, se tratará de aproximar los términos de tiempo y sustancia para definir la forma. Ello conllevará al estudio de las notables patologías derivadas de la asunción de un tiempo cronológico en nuestra contemporaneidad frente a las cuales, las intuiciones contenidas en Mérida, se alinearán con la actual actitud revisionista en el ámbito del pensamiento filosófico y científico. En Mérida, la memoria recogerá los aspectos de la conciencia así como los aspectos vinculados a la experiencia íntima y colectiva como soporte para la consecución de un discurso. La dualidad entre intuición e inteligencia será recogida por Moneo con idea de trascender su incomunicabilidad, mediante una operación que consistirá en la reivindicación de una memoria irreductible, cuya morada estaría incardinada en el propio tiempo de la duración y de la vida y no en la espacialidad coextensiva del presente y de la acción funcional sobre la materia. Moneo asumirá el papel de la memoria como condición central de una forma que se encarnará al concebirse como un teatro. En la respuesta a la contradicción entre el hecho físico y el efecto psíquico de la experiencia humana residirá la pertinencia de un tiempo narrativo. Será entonces el lenguaje el encargado de aportar sentido a la obra mediante el recurso fundado en la dramatización de la experiencia, es decir, a través de una conexión entre la conciencia íntima y el carácter social y colectivo intrínseco en la arquitectura. ABSTRACT TIME AS A SUBSTANCE OF FORM. AN APPROACH TO THE ROMAN ART MUSEUM OF MÉRIDA FROM THE VIEWPOINT OF VITALISM. The dominant model during the Modern Era placed man as a subject inside the great mechanism of the cosmos. It is also based in an idea about natural being within the ontological tradition initiated by the pre-Socratic Eleatism that conceives it as something immutable and static in respect with change and movement, which are considered as mere appearances. Prior to the emergence of the great Greek philosophers occurred a transformation where concepts of cosmology linked to a primordial time, changed to a view of the universe as indestructible, timeless, unchanging, perfect, geometric and spatial. If Democritus accepted a universe subjected to randomness and necessity, Plato thought that the universe only worked by necessity. This ontological model is called into question when man is not conceived as a piece of a broader system, but as a radical center of thinking. The radical condition of man then is his own life. This is the core concept of so-called Vitalism, whose most influential representative in Spain was José Ortega y Gasset. The stillness of being – of man - loses its meaning; in the words of Ortega, “it is not being but being in progress” that characterizes human life. The Cartesian reason is now the vital reason and its subject of study is no longer nature but its own evolution, in other words, time and history. This approach is fundamental to understand the building which is the subject of this study, the Museum of Roman Art in Mérida (1980-1985) by Rafael Moneo. The concept of time is used as a framework and structure of this thesis, demonstrating the notorious and very significant role this building has implied in the career of its author and in the national and international panorama of architecture and museology. This project allow us to approach the thought of its author through a building that, even whilst widely recognized, does not yet have a sufficiently comprehensive study covering its breadth and richness. This thesis is not a compendium of what already has been researched on Merida; it is a global and interpretative approach whose meaning can only be conceived as a study of its complete structure in line with the vital, historical and narrative logos the project implies. We will review the historical idea where spatial configuration of the form would have had primacy with respect to temporary configuration, because the latter refers to a spatial and circumstantial condition. The vicarious nature of the circumstance will be elevated by Ortega to the category of essential, thus showing a paradox which reformulation leads us to the conception of a substantial time. The dictionary of the Spanish Royal Academy, in its third meaning, defines substance as "that which remains in something that changes". This is a reference to ancient thought. It will be shown that what remains does not necessarily imply a static and Eleatic conception of form. It will also be shown that the essential architecture is not uniquely the timeless architecture of Platonism and that it is possible to conceive the "firmitas" parallel to the "durée" of Henri Bergson. As a result of this traditional association between substance and stillness, it marginalizes the time and the duration to the non-substantial; for this reason, we will try to approach terms of time and substance to define the shape. This will involve studying significant pathologies resulting from an assumption of chronological time in our contemporary world against which, the insights contained in Merida, will be aligned with the current revisionist attitude in the fields of philosophical and scientific thought. In Merida, memory includes aspects of consciousness as well as aspects linked to the intimate and collective experience as a foundation for the achievement of discourse. The duality between intuition and intelligence is put forward by Moneo with the idea of transcending its lack of communication, by means of a resource consisting of the vindication of an irreducible memory, whose home would be embodied in the time of duration and life and not in the coextensive spatiality of the present and in the functional action on the matter. Moneo demonstrates the role of memory as a central condition of form as a theatre. In response to the contradiction between the physical fact and the psychological effect of human experience lies the relevance of narrative time. Language then assumes the responsibility of giving meaning to the work through the dramatization of experience, i.e., through a connection between the intimate consciousness and the intrinsic social and collective character of architecture.

Detection of 400-year-old Yersinia pestis DNA in human dental pulp: An approach to the diagnosis of ancient septicemia

Ancient septicemic plague epidemics were reported to have killed millions of people for 2 millenniums. However, confident diagnosis of ancient septicemia solely on the basis of historical clinical observations is not possible. The lack of suitable infected material has prevented direct demonstration of ancient septicemia; thus, the history of most infections such as plague remains hypothetical. The durability of dental pulp, together with its natural sterility, makes it a suitable material on which to base such research. We hypothesized that it would be a lasting refuge for Yersinia pestis, the plague agent. DNA extracts were made from the dental pulp of 12 unerupted teeth extracted from skeletons excavated from 16th and 18th century French graves of persons thought to have died of plague (“plague teeth”) and from 7 ancient negative control teeth. PCRs incorporating ancient DNA extracts and primers specific for the human β-globin gene demonstrated the absence of inhibitors in these preparations. The incorporation of primers specific for Y. pestis rpoB (the RNA polymerase β-subunit-encoding gene) and the recognized virulence-associated pla (the plasminogen activator-encoding gene) repeatedly yielded products that had a nucleotide sequence indistinguishable from that of modern day isolates of the bacterium. The specific pla sequence was obtained from 6 of 12 plague skeleton teeth but 0 of 7 negative controls (P < 0.034, Fisher exact test). A nucleic acid-based confirmation of ancient plague was achieved for historically identified victims, and we have confirmed the presence of the disease at the end of 16th century in France. Dental pulp is an attractive target in the quest to determine the etiology of septicemic illnesses detected in ancient corpses. Molecular techniques could be applied to this material to resolve historical outbreaks.

Histone underacetylation is an ancient component of mammalian X chromosome inactivation

Underacetylation of histone H4 is thought to be involved in the molecular mechanism of mammalian X chromosome inactivation, which is an important model system for large-scale genetic control in eukaryotes. However, it has not been established whether histone underacetylation plays a critical role in the multistep inactivation pathway. Here we demonstrate differential histone H4 acetylation between the X chromosomes of a female marsupial, Macropus eugenii. Histone underacetylation is the only molecular aspect of X inactivation known to be shared by marsupial and eutherian mammals. Its strong evolutionary conservation implies that, unlike DNA methylation, histone underacetylation was a feature of dosage compensation in a common mammalian ancestor, and is therefore likely to play a central role in X chromosome inactivation in all mammals.

An ancient family of human endogenous retroviruses encodes a functional homolog of the HIV-1 Rev protein

The human endogenous retrovirus K (HERV-K) family of endogenous retroviruses consists of ≈50 proviral copies per haploid human genome. Herein, the HERV-Ks are shown to encode a sequence-specific nuclear RNA export factor, termed K-Rev, that is functionally analogous to the HIV-1 Rev protein. Like HIV-1 Rev, K-Rev binds to both the Crm1 nuclear export factor and to a cis-acting viral RNA target to activate nuclear export of unspliced RNAs. Surprisingly, this HERV-K RNA sequence, which is encoded within the HERV-K long terminal repeat, is also recognized by HIV-1 Rev. These data provide surprising evidence for an evolutionary link between HIV-1 and a group of endogenous retroviruses that first entered the human genome ≈30 million years ago.

Carbonic anhydrase is an ancient enzyme widespread in prokaryotes

Carbonic anhydrases catalyze the reversible hydration of CO2 and are ubiquitous in highly evolved eukaryotes. The recent identification of a third class of carbonic anhydrase (γ class) in a methanoarchaeon and our present finding that the β class also extends into thermophilic species from the Archaea domain led us to initiate a systematic search for these enzymes in metabolically and phylogenetically diverse prokaryotes. Here we show that carbonic anhydrase is widespread in the Archaea and Bacteria domains, and is an ancient enzyme. The occurrence in chemolithoautotrophic species occupying deep branches of the universal phylogenetic tree suggests a role for this enzyme in the proposed autotrophic origin of life. The presence of the β and γ classes in metabolically diverse species spanning the Archaea and Bacteria domains demonstrates that carbonic anhydrases have a far more extensive and fundamental role in prokaryotic biology than previously recognized.

Ancient mtDNA sequences in the human nuclear genome: A potential source of errors in identifying pathogenic mutations

Nuclear-localized mtDNA pseudogenes might explain a recent report describing a heteroplasmic mtDNA molecule containing five linked missense mutations dispersed over the contiguous mtDNA CO1 and CO2 genes in Alzheimer’s disease (AD) patients. To test this hypothesis, we have used the PCR primers utilized in the original report to amplify CO1 and CO2 sequences from two independent ρ° (mtDNA-less) cell lines. CO1 and CO2 sequences amplified from both of the ρ° cells, demonstrating that these sequences are also present in the human nuclear DNA. The nuclear pseudogene CO1 and CO2 sequences were then tested for each of the five “AD” missense mutations by restriction endonuclease site variant assays. All five mutations were found in the nuclear CO1 and CO2 PCR products from ρ° cells, but none were found in the PCR products obtained from cells with normal mtDNA. Moreover, when the overlapping nuclear CO1 and CO2 PCR products were cloned and sequenced, all five missense mutations were found, as well as a linked synonymous mutation. Unlike the findings in the original report, an additional 32 base substitutions were found, including two in adjacent tRNAs and a two base pair deletion in the CO2 gene. Phylogenetic analysis of the nuclear CO1 and CO2 sequences revealed that they diverged from modern human mtDNAs early in hominid evolution about 770,000 years before present. These data would be consistent with the interpretation that the missense mutations proposed to cause AD may be the product of ancient mtDNA variants preserved as nuclear pseudogenes.

Intron positions correlate with module boundaries in ancient proteins

We analyze the three-dimensional structure of proteins by a computer program that finds regions of sequence that contain module boundaries, defining a module as a segment of polypeptide chain bounded in space by a specific given distance. The program defines a set of “linker regions” that have the property that if an intron were to be placed into each linker region, the protein would be dissected into a set of modules all less than the specified diameter. We test a set of 32 proteins, all of ancient origin, and a corresponding set of 570 intron positions, to ask if there is a statistically significant excess of intron positions within the linker regions. For 28-Å modules, a standard size used historically, we find such an excess, with P < 0.003. This correlation is neither due to a compositional or sequence bias in the linker regions nor to a surface bias in intron positions. Furthermore, a subset of 20 introns, which can be putatively identified as old, lies even more explicitly within the linker regions, with P < 0.0003. Thus, there is a strong correlation between intron positions and three-dimensional structural elements of ancient proteins as expected by the introns-early approach. We then study a range of module diameters and show that, as the diameter varies, significant peaks of correlation appear for module diameters centered at 21.7, 27.6, and 32.9 Å. These preferred module diameters roughly correspond to predicted exon sizes of 15, 22, and 30 residues. Thus, there are significant correlations between introns, modules, and a quantized pattern of the lengths of polypeptide chains, which is the prediction of the “Exon Theory of Genes.”

Fish and mammals in the economy of an ancient Peruvian kingdom

Fish and mammal bones from the coastal site of Cerro Azul, Peru shed light on economic specialization just before the Inca conquest of A.D. 1470. The site devoted itself to procuring anchovies and sardines in quantity for shipment to agricultural communities. These small fish were dried, stored, and eventually transported inland via caravans of pack llamas. Cerro Azul itself did not raise llamas but obtained charqui (or dried meat) as well as occasional whole adult animals from the caravans. Guinea pigs were locally raised. Some 20 species of larger fish were caught by using nets; the more prestigious varieties of these show up mainly in residential compounds occupied by elite families.

Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes

Isopentenyl diphosphate (IPP) is the central intermediate in the biosynthesis of isoprenoids, the most ancient and diverse class of natural products. Two distinct routes of IPP biosynthesis occur in nature: the mevalonate pathway and the recently discovered deoxyxylulose 5-phosphate (DXP) pathway. The evolutionary history of the enzymes involved in both routes and the phylogenetic distribution of their genes across genomes suggest that the mevalonate pathway is germane to archaebacteria, that the DXP pathway is germane to eubacteria, and that eukaryotes have inherited their genes for IPP biosynthesis from prokaryotes. The occurrence of genes specific to the DXP pathway is restricted to plastid-bearing eukaryotes, indicating that these genes were acquired from the cyanobacterial ancestor of plastids. However, the individual phylogenies of these genes, with only one exception, do not provide evidence for a specific affinity between the plant genes and their cyanobacterial homologues. The results suggest that lateral gene transfer between eubacteria subsequent to the origin of plastids has played a major role in the evolution of this pathway.

Ancient origin of pathogen recognition specificity conferred by the tomato disease resistance gene Pto

We have investigated the origin of the Pto disease resistance (R) gene that was previously identified in the wild tomato species Lycopersicon pimpinellifolium and isolated by map-based cloning. Pto encodes a serine-threonine protein kinase that specifically recognizes strains of Pseudomonas syringae pv. tomato (Pst) that express the avirulence gene avrPto. We examined an accession of the distantly related wild species Lycopersicon hirsutum var. glabratum that exhibits avrPto-specific resistance to Pst. The Pst resistance of L. hirsutum was introgressed into a susceptible Lycopersicon esculentum background to create the near-isogenic line 96T133-3. Resistance to Pst(avrPto) in 96T133-3 was inherited as a single dominant locus and cosegregated with a restriction fragment length polymorphism detected by the Pto gene. This observation suggested that a member of the Pto gene family confers Pst(avrPto) resistance in this L. hirsutum line. Here we report the cloning and characterization of four members of the Pto family from 96T133-3. One gene (LhirPto) is 97% identical to Pto and encodes a catalytically active protein kinase that elicits a hypersensitive response when coexpressed with avrPto in leaves of Nicotiana benthamiana. In common with the Pto kinase, the LhirPto protein physically interacts with AvrPto and downstream members of the Pto signaling pathway. Our studies indicate that R genes of the protein kinase class may not evolve rapidly in response to pathogen pressure and rather that their ability to recognize specific Avr proteins can be highly conserved.

Ancient Maya documents concerning the movements of Mars

A large part of the pre-Columbian Maya book known as the Dresden Codex is concerned with an exploration of commensurate relationships among celestial cycles and their relationship to other, nonastronomical cycles of cultural interest. As has long been known, pages 43b–45b of the Codex are concerned with the synodic cycle of Mars. New work reported here with another part of the Codex, a complex table on pages 69–74, reveals a concern on the part of the ancient Maya astronomers with the sidereal motion of Mars as well as with its synodic cycle. Two kinds of empiric sidereal intervals of Mars were used, a long one (702 days) that included a retrograde loop and a short one that did not. The use of these intervals, which is indicated by the documents in the Dresden Codex, permitted the tracking of Mars across the zodiac and the relating of its movements to the terrestrial seasons and to the 260-day sacred calendar. While Kepler solved the sidereal problem of Mars by proposing an elliptical heliocentric orbit, anonymous but equally ingenious Maya astronomers discovered a pair of time cycles that not only accurately described the planet's motion, but also related it to other cosmic and terrestrial concerns.

The Sm domain is an ancient RNA-binding motif with oligo(U) specificity

Sm and Sm-like proteins are members of a family of small proteins that is widespread throughout eukaryotic kingdoms. These proteins form heteromers with one another and bind, as heteromeric complexes, to various RNAs, recognizing primarily short U-rich stretches. Interestingly, completion of several genome projects revealed that archaea also contain genes that may encode Sm-like proteins. Herein, we studied the properties of one Sm-like protein derived from the archaebacterium Archaeoglobus fulgidus and overexpressed in Escherichia coli. This single small protein closely reflects the properties of an Sm or Sm-like protein heteromer. It binds to RNA with a high specificity for oligo(U), and assembles onto the RNA to form a complex that exhibits, as judged by electron microscopy, a ring-like structure similar to the ones observed with the Sm core ribonucleoprotein and the like Sm (LSm) protein heteromer. Importantly, multivariate statistical analysis of negative-stain electron-microscopic images revealed a sevenfold symmetry for the observed ring structure, indicating that the proteins form a homoheptamer. These results support the structural model of the Sm proteins derived from crystallographic studies on Sm heterodimers and demonstrate that the Sm protein family evolved from a single ancestor that was present before the eukaryotic and archaeal kingdoms separated.

Global biodiversity and the ancient carbon cycle

Paleontological data for the diversity of marine animals and land plants are shown to correlate significantly with a concurrent measure of stable carbon isotope fractionation for approximately the last 400 million years. The correlations can be deduced from the assumption that increasing plant diversity led to increasing chemical weathering of rocks and therefore an increasing flux of carbon from the atmosphere to rocks, and nutrients from the continents to the oceans. The CO2 concentration dependence of photosynthetic carbon isotope fractionation then indicates that the diversification of land plants led to decreasing CO2 levels, while the diversification of marine animals derived from increasing nutrient availability. Under the explicit assumption that global biodiversity grows with global biomass, the conservation of carbon shows that the long-term fluctuations of CO2 levels were dominated by complementary changes in the biological and fluid reservoirs of carbon, while the much larger geological reservoir remained relatively constant in size. As a consequence, the paleontological record of biodiversity provides an indirect estimate of the fluctuations of ancient CO2 levels.