Evolution

ORI-GENE: gene classification based on the evolutionary tree.

by Hideaki Mizuno

Mizuno H, Tanaka Y, Nakai K, Sarai A. Bioinformatics. 2001, 17:167-73.

MOTIVATION:
Genome projects have produced large amounts of data on the sequences of new genes whose functions are... more MOTIVATION:
Genome projects have produced large amounts of data on the sequences of new genes whose functions are as yet unknown. The functions of new genes are usually inferred by comparing their sequences with those of known genes, but evaluation of the sequence homology of individual genes does not make the most of the available sequence information. Therefore, new methods and tools for extracting more biological information from homology searches would be advantageous.
RESULTS:
We have developed a computational tool, ORI-GENE, to analyze the results of sequence homology searches from the perspective of the evolution of selected sets of new genes. ORI-GENE has a graphical interface and accomplishes two important tasks: first, based on the output of homology searches, it identifies species with similar genes and displays their pattern of distribution on the phylogenetic tree. This function enables one to infer the way in which a given gene may have propagated among species over time. Second, from the distribution patterns, it predicts the point at which a given gene may have been first acquired (i.e. its 'origin'), then classifies the gene on that basis. Because it makes use of available evolutionary information to show the way in which genes cluster among species, ORI-GENE should be an effective tool for the screening and classification of new genes revealed by genome analysis.
AVAILABILITY:
ORI-GENE is retrievable via the Internet at: http://www.rtc.riken.go.jp/jouhou/ORI-GENE.

Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome

by Hideaki Mizuno

Mizuno H, Atwal G, Wang H, Levine AJ, Vazquez A. BMC Genetics 2010, 11:27.

Background
The creation of a coherent genomic map of recent selection is one of the greatest challenges towards a... more Background
The creation of a coherent genomic map of recent selection is one of the greatest challenges towards a better understanding of human evolution and the identification of functional genetic variants. Several methods have been proposed to detect linkage disequilibrium (LD), which is indicative of natural selection, from genome-wide profiles of common genetic variations but are designed for large regions.

Results
To find population-specific LD within small regions, we have devised an entropy-based method that utilizes differences in haplotype frequency between populations. The method has the advantages of incorporating multilocus association, conciliation with low allele frequencies, and independence from allele polarity, which are ideal for short haplotype analysis. The comparison of HapMap SNPs data from African and Caucasian populations with a median resolution size of ~23 kb gave us novel candidates as well as known selection targets. Enrichment analysis for the yielded genes showed associations with diverse diseases such as cardiovascular, immunological, neurological, and skeletal and muscular diseases. A possible scenario for a selective force is discussed. In addition, we have developed a web interface (ENIGMA, available at http://gibk21.bse.kyutech.ac.jp/ENIGMA/index.html webcite), which allows researchers to query their regions of interest for population-specific LD.

Conclusion
The haplotype entropy method is powerful for detecting population-specific LD embedded in short regions and should contribute to further studies aiming to decipher the evolutionary histories of modern humans.

Misyurov D.A. Dialectical formulas based on the binary notation as the development formulas // Credo New. 2012. №2

by Dmitry Misyurov

The article suggests dialectical formulas based on the binary notation as the development formulas: formula with... more The article suggests dialectical formulas based on the binary notation as the development formulas: formula with dominant and the non-dominant elements; universal formula; formula with symbolic weight of elements; tautological formula. For example, it suggests an opportunity to use the dialectical formulas for modeling and artificial intelligence creation, etc.

Engineering love

by Brian Earp

Savulescu, J. and Sandberg, A. (2012). Love machine: Engineering lifelong romance. New Scientist, 2864, 28-29.

Essay partially adapted from Earp, B. D., Sandberg, A., and Savulescu, J. (2012). Natural selection, childrearing, and the ethics of marriage (and divorce): Building a case for the neuroenhancement of human relationships. Philosophy & Technology, forthcoming [see "profile" box in article].

Available at the New Scientist website: http://www.newscientist.com/article/mg21428646.200-love-machine-engineering-lifelong-romance.html

New Scientist BIG IDEA section, May 2012.

With break-up and divorce a major part of modern life, it looks... more New Scientist BIG IDEA section, May 2012.

With break-up and divorce a major part of modern life, it looks like we may be outliving our inborn capacity to love. But there could be a way to outwit evolution and make love last.

Also available at New Scientist: http://www.newscientist.com/article/mg21428646.200-love-machine-engineering-lifelong-romance.html.

Defining biominerals and organominerals: direct and indirect indicators of life

by Martin Brasier

Evolutionary Pressures and Environment's building.

by Laura Desirée Di Paolo

A cryptic intermediate in the evolution of chameleon tongue projections

by Kurt Schwenk

Function and the Evolution of Phenotypic Stability: Connecting Pattern to Process

by Kurt Schwenk

Constraint

by Kurt Schwenk

Molecular preservation of the pigment melanin in fossil melanosomes.

by Engdahl Anders

Fossil feathers, hairs and eyes are regularly preserved as carbonized traces comprised of masses of micrometre-sized... more Fossil feathers, hairs and eyes are regularly preserved as carbonized traces comprised of masses of micrometre-sized bodies that are spherical, oblate or elongate in shape. For a long time, these minute structures were regarded as the remains of biofilms of keratinophilic bacteria, but recently they have been reinterpreted as melanosomes; that is, colour-bearing organelles. Resolving this fundamental difference in interpretation is crucial: if endogenous then the fossil microbodies would represent a significant advancement in the fields of palaeontology and evolutionary biology given, for example, the possibility to reconstruct integumentary colours and plumage colour patterns. It has previously been shown that certain trace elements occur in fossils as organometallic compounds, and hence may be used as biomarkers for melanin pigments. Here we expand this knowledge by demonstrating the presence of molecularly preserved melanin in intimate association with melanosome-like microbodies isolated from an argentinoid fish eye from the early Eocene of Denmark.

Molecular preservation of the pigment melanin in fossil melanosomes.

by Engdahl Anders

Fossil feathers, hairs and eyes are regularly preserved as carbonized traces comprised of masses of micrometre-sized... more Fossil feathers, hairs and eyes are regularly preserved as carbonized traces comprised of masses of micrometre-sized bodies that are spherical, oblate or elongate in shape. For a long time, these minute structures were regarded as the remains of biofilms of keratinophilic bacteria, but recently they have been reinterpreted as melanosomes; that is, colour-bearing organelles. Resolving this fundamental difference in interpretation is crucial: if endogenous then the fossil microbodies would represent a significant advancement in the fields of palaeontology and evolutionary biology given, for example, the possibility to reconstruct integumentary colours and plumage colour patterns. It has previously been shown that certain trace elements occur in fossils as organometallic compounds, and hence may be used as biomarkers for melanin pigments. Here we expand this knowledge by demonstrating the presence of molecularly preserved melanin in intimate association with melanosome-like microbodies isolated from an argentinoid fish eye from the early Eocene of Denmark.

Van Dijk, E.M. & Kattmann, U. (2008). Biologieunterricht in naturgeschichtlicher Perspektive: Zur Reform auf der Sekundarstufe I, Teil II: Umsetzung. Mathematischer und Naturwissenschaftlicher Unterricht, 61 (2), 107-114. (Reprinted in ‘Sonderausgabe Evolution’ (pp. 60-66), Mathematischer und Naturwissenschaftlicher Unterricht).

by Esther van Dijk

Mit der Umgestaltung des Unterrichts auf der Sekundarstufe I soll kumulatives, d. h. sinnvoll aufeinander aufbauendes... more Mit der Umgestaltung des Unterrichts auf der Sekundarstufe I soll kumulatives, d. h. sinnvoll aufeinander aufbauendes Lernen gefördert und damit die traditionelle Zersplitterung des Biologieunterrichts in Einzelthemen überwunden werden. In Teil I wurde begründet, dass die Evolutionstheorie möglichst früh in den Unterricht einzuführen ist und als durchgehendes Erklärungsprinzip angewendet werden sollte. Im vorliegenden Teil II wird diese Konzeption anhand einer Sequenz von Unterrichtseinheiten und der sich ergebenden Vernetzung konkretisiert.

Van Dijk, E.M. & Kattmann, U. (2008). Biologieunterricht in naturgeschichtlicher Perspektive: Zur Reform auf der Sekundarstufe I, Teil I: Grundlagen. Mathematischer und Naturwissenschaftlicher Unterricht, 61 (1), 12-15. (Reprinted in ‘Sonderausgabe Evolution’ (pp. 56-60), Mathematischer und Naturwissenschaftlicher Unterricht).

by Esther van Dijk

Mit Umgestaltung des Unterrichts auf der Sekundarstufe I gelangen zusammen mit neuen Orientierungen alte Probleme... more Mit Umgestaltung des Unterrichts auf der Sekundarstufe I gelangen zusammen mit neuen Orientierungen alte Probleme erneut auf die Tagesordnung. Die Orientierung an Basiskonzepten und Kompetenzen soll kumulatives, d. h. sinnvoll aufeinander aufbauendes Lernen fördern und damit die traditionelle Zersplitterung des Biologieunterrichts in Einzelthemen überwinden. Dabei gewinnt das Konzept, Erklärungen der Evolutionstheorie und das Thema Evolution selbst möglichst früh in den Unterricht einzuführen, zunehmend
an Bedeutung. Stärker als bisher sollte dabei ein durchgehendes Konzept verfolgt und der Charakter der Biologie als historischer Wissenschaft beachtet werden. Eine Sequenz von Unterrichtsentwürfen wird hierzu in Teil II beschrieben.

Van Dijk, E.M. & Kattmann, U. (2009). Teaching evolution with historical narratives. Evolution: Education and Outreach, 2, 479-489.

by Esther van Dijk

This paper focuses on evolution as a unifying theme in biology education. Our aim is to argue that the different... more This paper focuses on evolution as a unifying theme in biology education. Our aim is to argue that the different topics taught in secondary school biology classes should be enriched with and linked together by means of accounts of the history of life. We named this approach a “natural history perspective” on biology education. An essential aspect of the natural history perspective is the claim that evolutionary history forms the context for the
development of an understanding of evolutionary processes. While there are some indications that a natural history perspective can function as a context for understanding micro-evolutionary processes, more research is called for.

Van Dijk, E.M. & Reydon, T.A.C. (2010). A conceptual analysis of evolutionary theory for teacher education. Science & Education, 19, 655-677.

by Esther van Dijk

In this paper we present a schematic overview of the central concepts in evolutionary theory, setting them off against... more In this paper we present a schematic overview of the central concepts in evolutionary theory, setting them off against the background of widespread misconceptions about them. Our aim is to provide high school teachers with (1) an overview of those
particular concepts that they can expect students to have difficulties with, (2) a comparison of students’ alternative conceptions with the corresponding accepted scientific concepts and (3) some recommendations for teaching these concepts. We aim to improve the learning and teaching of evolution by making the relevant conceptual debates within the
fields of history and philosophy of science more accessible to science teachers. We intended this conceptual analysis to be of use as a teaching tool for in-service teachers, as well as biology teachers in training.

Can the Quran Support Darwin? An Evolutionist Approach by Two Turkish Scholars after the Foundation of the Turkish Republic

by veysel kaya

The Muslim World 102/2 (2012), p. 357-370.

PyPop update--a software pipeline for large-scale multilocus population genomics

by Alex Lancaster

Kalafatidis, G., & Kalogiannakis, M. (2011). Evolution theory by natural selection in education: the case of fossils. Towards a new framework for the appointment of students’ perceptions for the realization of cognitive conflict, Science Education Research and Praxis, 36-37, 50-63 (in Greek).

by Michail Kalogiannakis

In the present research, we are trying to find out whether palaeontology is the appropriate phenomenological context... more In the present research, we are trying to find out whether palaeontology is the appropriate phenomenological context for the students to show their beliefs about the cognitive conflict. In addition, suggestions about the transition from the practical-experiential knowledge to the scholar version of the scientific knowledge are presented. If students want to observe the “story of life”, they have to surpass important notional obstacles which are connected to archetypal ways of thinking, among which the Lamarckian model is outstanding. Based on an appropriately designed questionnaire which was addressed to second-year students of junior high school, we found out that approximately one out of seven students believes that fossils are dinosaurs’ bones and one out of six students seems to believe that once dinosaurs co-existed with humans and one out of eight believes that the reason of dinosaurs’ extinction was human-made pollution. It is remarkable that only a really small percentage of students has realized that biological evolution is due to cumulative changes which occur in a population as time goes by.
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Καλαφατίδης, Γ., & Καλογιαννάκης, Μ. (2011). Η θεωρία της εξέλιξης μέσω της φυσικής επιλογής στην εκπαίδευση: η περίπτωση των απολιθωμάτων. Προς ένα νέο πλαίσιο για την ανάδειξη των αντιλήψεων των μαθητών/τριών για την πραγματοποίηση γνωστικής σύγκρουσης, Διδασκαλία των Φυσικών Επιστημών - Έρευνα και Πράξη, 36-37, 5-17.

Στα πλαίσια της παρούσας έρευνας επιχειρούμε να διαπιστώσουμε κατά πόσον η παλαιοντολογία αποτελεί το κατάλληλο φαινομενολογικό πλαίσιο για την ανάδειξη των αντιλήψεων των μαθητών για την πραγματοποίηση γνωστικής σύγκρουσης. Επίσης, παρουσιάζονται προτάσεις για τη μετάβαση από την πρακτικοβιωματική γνώση στη σχολική εκδοχή της επιστημονικής γνώσης. Οι μαθητές προκειμένου να παρακολουθήσουν την «ιστορία της ζωής», πρέπει να υπερβούν σημαντικά εννοιολογικά εμπόδια που συνδέονται με αρχέτυπους τρόπους σκέψης και μεταξύ αυτών των εμποδίων δεσπόζει το λαμαρκιανό μοντέλο. Με βάση κατάλληλα δομημένο ερωτηματολόγιο απευθυνόμενο σε μαθητές Β΄ Γυμνασίου διαπιστώσαμε ότι ένας στους επτά περίπου μαθητές πιστεύει ότι τα απολιθώματα είναι οστά δεινοσαύρων και ένας στους έξι μαθητές φαίνεται να πιστεύει ότι οι δεινόσαυροι κάποτε συνυπήρχαν με τους ανθρώπους και ένας στους οκτώ ότι η αιτία της εξαφάνισης τους ήταν η ανθρωπογενής ρύπανση. Είναι αξιοσημείωτο ότι μόνο ένα ελάχιστο ποσοστό μαθητών έχει αντιληφθεί ότι η βιολογική εξέλιξη αναφέρεται σε αθροιστικές αλλαγές, που συμβαίνουν σ’ ένα πληθυσμό, με το πέρασμα του χρόνου.

BIOCHEMISTRY AND PHARMACOLOGY OF COLUBRID SNAKE VENOMS

by Stephen Mackessy

Published in Journal of Toxicology-Toxin Reviews 2002

The polyphyletic family Colubridae contains approximately
two-thirds of the described species of advanced... more The polyphyletic family Colubridae contains approximately
two-thirds of the described species of advanced snakes, and
nearly half of these (approx. 700 species) produce a venom in a specialized cephalic gland, the Duvernoy’s gland. Biochemical and pharmacological information is lacking for venoms of most species, and modest detailed information on venom composition is available for only a few species which represent a potential health threat to humans. However, colubrid venoms represent a vast source of novel compounds, and some toxins, such as the 20–26 kD CRISP-related venom proteins (helveprins), have only recently been identified in both colubrid and elapid/viperid venoms. Difficulties associated with extraction have been addressed, and it is now possible to obtain venom sufficient for many analyses from even small species. There appears to be a greater number of venom components shared among the colubrids
and the front-fanged snakes than has been previously
noted, and it is probable that as analytical methods improve,
more similarities will emerge. It is clear that colubrid venoms
are homologous with front-fanged snake venoms, but overall
composition as well as biological role(s) of colubrid venoms
may be quite different. Metallo- and serine proteases have been identified in several colubrid venoms, and phospholipase A2 is a more frequent component than has been previously recognized. Venom phosphodiesterase, acetylcholinesterase and prothrombin activator activities occur in some venoms, and postsynaptic neurotoxins and myotoxins have been partially characterized for venoms from several species. Some venoms show high toxicity toward inbred mice, and others are toxic to birds and/or frogs only. Because many colubrids feed on non-mammalian prey, lethal toxicity toward mice is likely only relevant as a measure of potential risk posed to humans. Development of a non-mammalian vertebrate animal model would greatly facilitate systematic comparisons of the pharmacology of colubrid venoms and their components, and such a model would be more appropriate for evaluation of colubrid venom toxicity. Proteomics has the potential to increase our understanding of these venoms rapidly, but classical approaches to toxinology can also contribute
tremendously to this understudied field. As more colubrid
venoms are analyzed, new compounds unique to colubrid
venoms will be identified, and this work in turn will lead to a
better understanding of the evolution and biological significance of snake venoms and venom components.

maladapting minds book review

by dieneke hubbeling