Saturday, 26 July 2014

Welcome to my site...

Welcome to Hasan's Thoughts Dissected. You will find a panoply of articles on a range of topics and questions concerning human existence, knowledge and empirical inquiry. Most posts are organised under the following major subcategories:

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Evolution: Exploring the diversity and history of life on earth; the evidence for common ancestry, macroevolutionary transitions, phylogenetics and special topics such as the evolution of social behaviour.

Origin of Life: Building together a unified view of prebiotic chemistry; open problems in abiogenesis research and models of the origin of life including (but not excluded to) the RNA world, Iron-Suplhur world, the origin of biological information and other big ideas

Cosmology: Probing the origins, evolution and large scale structure of the observable universe and beyond. Topics include the formation of structure, quantum gravity, general relativity, the cosmic microwave background, inflation and speculative theories of the universe.

Theoretical Physics: An inquiry into the fundamental nature of small-scale and high-energy physics: includes quantum mechanics, quantum field theory, string theory, supersymmetry and beyond. Investigation of particles, forces, symmetries and field theories with experimental and phenomenological implications.

Philosophy of Mind: Controversies regarding consciousness and mental states: a discussion of major schools of thought, physicalism vs non-physicalism, the hard problem of qualia, elimitivism, behaviourism, functionalism and more.

Philosophy of Religion: A critique of  popular and scholarly arguments for the existence of God(s). Implications of the naturalism vs. theism debate and open problems in professional theology.

Psychology:  An introduction to influential ideas in modern psychology and cognitive science; an encounter with major figures and thinkers. Review articles on mental development, intelligence, personality, sociology and mental disorders.

Pseudoscience:  Debunking claims of creationists, the intelligent design community and popular hoaxes.

Friday, 25 July 2014

Common Ancestry: An Introduction

A central tenet of evolutionary biology is the notion of common ancestry. The theory of descent with modification ultimately connects all organisms to a single common ancestor. Humans, butterflies, lettuce, and bacteria all trace their lineages back to the same primordial stock. The crucial evidence for universal common ancestry includes homology.

Why Common Ancestry Matters
Common ancestry is the conceptual foundation upon which all of modern biology, including biomedical science, is built. Because we are descended from the same ancestral lineage as monkeys, mice, baker’s yeast, and even bacteria, we share with these organisms numerous homologies in the internal machinery of our cells. This is why studies of other organisms can teach us about ourselves.
Consider work on mice and yeast by Kriston McGary and colleagues (2010) in the lab of Edward Marcotte. The researchers knew that because mice and yeast are derived from a common ancestor, we find not only many of the same genes in both creatures, but many of the same groups of genes working together to carry out biological functions—what we might call gene teams. The scientists thus guessed that a good place to look for genes associated with mammalian diseases would be on mouse gene teams whose members are also teammates in yeast. Using a database of genes known to occur in both mice and yeast, McGary and colleagues first identified gene teams as sets of genes associated with a particular phenotype. In mice the phenotype might be a disease. In yeast it might be sensitivity to a particular drug. The researchers then looked for mouse and yeast gene teams with overlapping membership.

Among the pairs of overlapping teams they found was a mouse team of eight genes known to be involved in the development of blood vessels (angiogenesis) and a yeast team of 67 genes known to influence sensitivity to the drug lovastatin. These teams formed a pair because of the five genes that belonged to both. The connection between the two teams suggested that both might be larger than previously suspected, and that more than just five genes might play for both. In particular, the 62 genes from the yeast lovastatin team not already known to belong to the mouse angiogenesis team might, in fact, be members. Starting with this list of 62 candidates, the researchers conducted experiments in frogs revealing a role in angiogenesis for at least five of the genes. Three more genes on the list turned out to have been identified already as angiogenesis genes, but had not been flagged as such in the researchers’ database. Eight hits in 62 tries is a much higher success rate than would have been expected had the researchers simply chosen genes at random and tested their influence on angiogenesis. In other words, McGary and colleagues used genetic data from yeast, an organism with neither blood nor blood vessels, to identify genes in mammals that influence blood vessel growth. Researchers in Marcotte’s lab have since exploited the overlap between the yeast lovastatin team and the mouse angiogenesis team to identify an antifungal drug as an angiogenesis inhibitor that may be useful
in treating cancer (Cha et al. 2012). That the theory of descent with modification is such a powerful research tool indicates that it has a thing or two going for it.