Category Archives: Γαῖα

The Gaia hypothesis, also known as Gaia theory or Gaia principle, proposes that organisms interact with their inorganic surroundings on Earth to form a self-regulating, complex system that contributes to maintaining the conditions for life on the planet. Topics of interest include how the biosphere and the evolution of life forms affect the stability of global temperature, ocean salinity, oxygen in the atmosphere and other environmental variables that affect the habitability of Earth.

Artificial Intelligence – Depth First Search(DFS)

Depth-first search (DFS) is an algorithm for traversing or searching tree or graph data structures. One starts at the root (selecting some arbitrary node as the root in the case of a graph) and explores as far as possible along each branch before backtracking.

A version of depth-first search was investigated in the 19th century by French mathematician Charles Pierre Trémaux[1] as a strategy for solving mazes.

Algorithmic Thoughts - Artificial Intelligence | Machine Learning | Neuroscience | Computer Vision

Okay! So this is my first blog post!

I will start by talking about the most basic solution to search problems, which are an integral part of artificial intelligence.

What the hell are search problems?

In simple language, search problems consist of a graph, a starting node and a goal(also a node). Our aim while solving a search problem is to get a path from the starting node to the goal.

Consider the diagram below, we want to get to the node G starting from the node S.

Which path will we get on solving the search problem? How do we get the path? This is where algorithms come into picture and answer all our questions! We will look at Depth First Search which can be seen as a brute force method of solving a search problem.

Creating the search tree

So how do we simplify this problem? If we…

View original post 623 more words

Mitochondrial Eve

Allan Charles Wilson (18 October 1934 – 21 July 1991) was a Professor of Biochemistry at the University of California, Berkeley, a pioneer in the use of molecular approaches to understand evolutionary change and reconstruct phylogenies, and a revolutionary contributor to the study of human evolution. He was one of the most controversial figures in post-war biology; his work attracted a great deal of attention both from within and outside the academic world. He is the only New Zealander to have won the MacArthur Fellowship.[1]

He is best known for experimental demonstration of the concept of the molecular clock (with his doctoral student Vincent Sarich), which was theoretically postulated by Linus Pauling and Emile Zuckerkandl, revolutionary insights into the nature of the molecular anthropology of higher primates and human evolution, called Mitochondrial Eve hypothesis (with his doctoral students Rebecca L. Cann and Mark Stoneking).[2][3]

Wilson joined the UC Berkeley faculty of biochemistry in 1964, and was promoted to full professor in 1972.[8] His first major scientific contribution was published as Immunological Time-Scale For Hominid Evolution in the journal Science in December 1967.[16] With his student Vincent Sarich,[17][18] he showed that evolutionary relationships of the humanspecies with other primates, in particular the Great Apes (chimpanzees, gorillas, and orangutans), could be inferred from molecular evidence obtained from living species, rather than solely from fossils of extinct creatures. Their microcomplement fixation method (see complement system) measured the strength of the immune reaction between an antigen(serum albumin) from one species and an antibody raised against the same antigen in another species. The strength of the antibody-antigen reaction was known to be stronger between more closely related species: their innovation was to measure it quantitatively among many species pairs as an “immunological distance“. When these distances were plotted against the divergence times of species pair with well-established evolutionary histories, the data showed that the molecular difference increased linearly with time, in what was termed a “molecular clock“. Given this calibration curve, the time of divergence between species pairs with unknown or uncertain fossil histories could be inferred. Most controversially, their data suggested that divergence times between humans, chimpanzees, and gorillas were on the order of 3~5 million years, far less than the estimates of 9~30 million years accepted by conventional paleoanthropologists from fossil hominids such as Ramapithecus. This ‘recent origin’ theory of human/ape divergence remained controversial until the discovery of the “Lucy” fossils in 1974.[15]

Wilson and another PhD student Mary-Claire King subsequently compared several lines of genetic evidence (immunology, amino acid differences, and protein electrophoresis) on the divergence of humans and chimpanzees, and showed that all methods agreed that the two species were >99% similar.[4][19] Given the large organismal differences between the two species in the absence of large genetic differences, King and Wilson argued that it was not structural gene differences that were responsible for species differences, butgene regulation of those differences, that is, the timing and manner in which near-identical gene products are assembled during embryology and development. In combination with the “molecular clock” hypothesis, this contrasted sharply with the accepted view that larger or smaller organismal differences were due to large or smaller rates of genetic divergence.

In the early 1980s, Wilson further refined traditional anthropological thinking with his work with PhD students Rebecca Cann and Mark Stoneking on the so-called “Mitochondrial Eve” hypothesis.[20] In his efforts to identify informative genetic markers for tracking human evolutionary history, he focused on mitochondrial DNA (mtDNA) — genes that are found in mitochondria in the cytoplasm of the cell outside the nucleus. Because of its location in the cytoplasm, mtDNA is passed exclusively from mother to child, the father making no contribution, and in the absence of genetic recombination defines female lineages over evolutionary timescales. Because it also mutates rapidly, it is possible to measure the small genetic differences between individual within species by restriction endonuclease gene mapping. Wilson, Cann, and Stoneking measured differences among many individuals from different human continental groups, and found that humans from Africa showed the greatest inter-individual differences, consistent with an African origin of the human species (the so-called “Out of Africa” hypothesis). The data further indicated that all living humans shared a common maternal ancestor, who lived in Africa only a few hundreds of thousands of years ago. This common ancestor became widely known in the media and popular culture as the Mitochondrial Eve. This had the unfortunate and erroneous implication that only a single female lived at that time, when in fact the occurrence of a coalescent ancestor is a necessary consequence of population genetic theory, and the Mitochondrial Eve would have been only one of many humans (male and female) alive at that time.[2][3] This finding was, like his earlier results, not readily accepted by anthropologists. Conventional hypothesis was that various human continental groups had evolved from diverse ancestors, over several million of years since divergence from chimpanzees. The mtDNA data, however, strongly suggested that all humans descended from a common, quite recent, African mother.[4][15]

Proc Natl Acad Sci U S A. 1969 Aug;63(4):1088-93.

A molecular time scale for human evolution.


We discuss published molecular evidence concerning the relationship of man to African apes and Old World monkeys. Quantitative comparisons of their serum albumins, transferrins, hemoglobins, and DNA show that man is genetically much more similar to the African apes than to the Old World monkeys. The amino acid sequences of hemoglobins from humans, chimpanzees, gorillas, and rhesus monkeys are consistent with the hypothesis that the probability of an amino acid substitution occurring in a given interval of time is the same for every hemoglobin lineage. This allows the use of these data as a hemoglobin evolutionary clock, just as we have previously done with the albumins. It is shown that concordance exists between the hemoglobin and albumin results and that both support the suggestion that the human lineage diverged from that leading to the African apes far more recently than is generally supposed. Considering both the albumin and hemoglobin data, we would set the most probable date at 4 to 5 million years.

[PubMed – indexed for MEDLINE]

Free PMC Article

Ocean Climate

Ocean acidification is the ongoing decrease in the pH of the Earth‘s oceans, caused by the uptake of carbon dioxide (CO2) from the atmosphere.[2] Seawater is slightly basic (meaning pH > 7), and the process in question is a shift towards pH-neutral conditions rather than a transition to acidic conditions (pH < 7).[3] Ocean alkalinity is not changed by the process, or may increase over long time periods due to carbonate dissolution.[4] An estimated 30–40% of the carbon dioxide from human activity released into the atmosphere dissolves into oceans, rivers and lakes.[5][6] To achieve chemical equilibrium, some of it reacts with the water to form carbonic acid. Some of these extra carbonic acid molecules react with a water molecule to give a bicarbonate ion and a hydronium ion, thus increasing ocean acidity (H+ ion concentration). Between 1751 and 1994 surface ocean pH is estimated to have decreased from approximately 8.25 to 8.14,[7] representing an increase of almost 30% in H+ion concentration in the world’s oceans.[8][9] Earth System Models project that within the last decade ocean acidity exceeded historical analogs[10] and in combination with other ocean biogeochemical changes could undermine the functioning of marine ecosystems and disrupt the provision of many goods and services associated with the ocean.[11]

Increasing acidity is thought to have a range of potentially harmful consequences for marine organisms, such as depressing metabolic rates and immune responses in some organisms, and causing coral bleaching.[citation needed] By increasing the presence of free hydrogen ions, each molecule of carbonic acid that forms in the oceans ultimately results in the conversion of two carbonate ions into bicarbonate ions. This net decrease in the amount of carbonate ions available makes it more difficult for marine calcifying organisms, such as coral and some plankton, to form biogenic calcium carbonate, and such structures become vulnerable to dissolution.[12] Ongoing acidification of the oceans threatens food chains connected with the oceans.[13][14] As members of theInterAcademy Panel, 105 science academies have issued a statement on ocean acidification recommending that by 2050, global CO2emissions be reduced by at least 50% compared to the 1990 level.[15]

While ongoing ocean acidification is anthropogenic in origin, it has occurred previously in Earth’s history.[16] The most notable example is the Paleocene-Eocene Thermal Maximum (PETM),[17] which occurred approximately 56 million years ago. For reasons that are currently uncertain, massive amounts of carbon entered the ocean and atmosphere, and led to the dissolution of carbonate sediments in all ocean basins.

Ocean acidification has been called the “evil twin of global warming[18][19][20][21][22] and “the other CO2 problem”.[19][21][23]


by DONALD PROTHERO on Dec 19 2012

Climate deniers try to distort or obfuscate the evidence about the changing atmosphere, and it’s not always easy to give overwhelmingly conclusive data that would convince them. In some cases the data are tricky to analyze, or do not have well-documented long-term histories necessary to answer every concern about whether recent weather events are truly unprecedented. The atmospheric system is very complicated, with many different processes operating on short-term, medium-term, and long-term time scales, and not all of it is as well understood as we would like. Thus, the arguments over changes in earth’s atmosphere often reach an impasse.

Not so for the oceans. Although oceans are an even larger system than the atmosphere, we understand them much better. More importantly, we have an excellent long-term record of how the oceans have changed over millions of years from thousands of deep-sea cores, and from the paleontological record of marine fossils that goes back over 700 million years. And unlike the atmospheres, oceans change very slowly over time, since the thermal inertia of water makes the seas very resistant to change except on long-term time scales. In addition, most ocean currents move slowly compared to atmospheric currents. So no matter what you want to make of the data showing atmospheric change, the changes in the oceans are more alarming, since oceans require immense stimuli to cause such change.