A Medley of Potpourri is just what it says; various thoughts, opinions, ruminations, and contemplations on a variety of subjects.
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Thursday, January 30, 2014
PubChemRDF is Launched
PubChem Blog
News, updates and tutorials about PubChem
Introducing PubChemRDF!
The PubChemRDF project encodes PubChem information using the Resource Description Framework (RDF). One of the aims of the PubChemRDF project is to help researchers work with PubChem data on local computing resources using semantic web technologies. Another aim is to harness ontological frameworks to help facilitate PubChem data sharing, analysis, and integration with resources external to the National Center for Biotechnology (NCBI) and across scientific domains.
What is RDF?
RDF stands for resource description framework and constitutes a family of World Wide Web Consortium (W3C) specifications for data interchange on the Web. RDF breaks down knowledge into machine readable discrete pieces, called “triples.” Each “triple” is organized as a trio of “subject-predicate-object.” For example, in the phrase “atorvastatin may treat hypercholesterolemia,” the subject is “atorvastatin,” the predicate is “may treat,” and the object is “hypercholesterolemia.” RDF uses a Uniform Resource Identifier (URI) to name each part of the “subject-predicate-object” triple. A URI looks just like a typical web URL.
RDF is a core part of semantic web standards. As an extension of the existing World Wide Web, the semantic web attempts to make it easier for users to find, share, and combine information. Semantic web leverages the following technologies: Extensible Markup Language (XML), which provides syntax for RDF; Web Ontology Language (OWL), which extends the ability of RDF to encode information; Resource Description Framework (RDF), which expresses knowledge; and RDF query language (SPARQL), which enables query and manipulation of RDF content.
How can PubChemRDF help your research?
PubChem users have frequently expressed interest in having a downloadable, schema-less database. PubChemRDF enables the NoSQL database access and query of PubChem databases. Using PubChemRDF, one can download the desired RDF formatted data files from the PubChem FTP site, import them into a triplestore, and query using a SPARQL query interface. There are a number of open-source or commercial triplestores, such as Apache Jena TDB and OpenLink Virtuoso (a list of triplestores can be found here: http://en.wikipedia.org/wiki/Triplestore).
Other than triplestores, PubChemRDF data can also be loaded into RDF-aware graph databases such as Neo4j, and the graph traversal algorithms can be used to query the RDF graphs. At last but not least, the ontological representation of PubChem knowledge base allows logical inference, such as forward/backward chaining.
The RDF data on the PubChem FTP site is arranged in such a way that you only need to download the type of information in which you are interested, so you can avoid downloading parts of PubChem data you will not use. For example, if you are just interested in computed chemical properties, you only need to download PubChemRDF data in compound descriptor subdomain. In addition to bulk download, PubChemRDF also provides programmatic data access through REST-full interface.
Where can you learn more about this?
To get an overview of the PubChemRDF project, please view this presentation. To learn more about detailed aspects of PubChemRDF and how to use it, please view this presentation. The PubChemRDF Release Notes provide additional technical information about the project.
Additional blog posts will follow on PubChemRDF project topics, including: the FTP site layout, the REST-full interface, and ways to utilize PubChemRDF for research purposes including using SPARQL queries.
The PubChemRDF project encodes PubChem information using the Resource Description Framework (RDF). One of the aims of the PubChemRDF project is to help researchers work with PubChem data on local computing resources using semantic web technologies. Another aim is to harness ontological frameworks to help facilitate PubChem data sharing, analysis, and integration with resources external to the National Center for Biotechnology (NCBI) and across scientific domains.
What is RDF?
RDF stands for resource description framework and constitutes a family of World Wide Web Consortium (W3C) specifications for data interchange on the Web. RDF breaks down knowledge into machine readable discrete pieces, called “triples.” Each “triple” is organized as a trio of “subject-predicate-object.” For example, in the phrase “atorvastatin may treat hypercholesterolemia,” the subject is “atorvastatin,” the predicate is “may treat,” and the object is “hypercholesterolemia.” RDF uses a Uniform Resource Identifier (URI) to name each part of the “subject-predicate-object” triple. A URI looks just like a typical web URL.
RDF is a core part of semantic web standards. As an extension of the existing World Wide Web, the semantic web attempts to make it easier for users to find, share, and combine information. Semantic web leverages the following technologies: Extensible Markup Language (XML), which provides syntax for RDF; Web Ontology Language (OWL), which extends the ability of RDF to encode information; Resource Description Framework (RDF), which expresses knowledge; and RDF query language (SPARQL), which enables query and manipulation of RDF content.
How can PubChemRDF help your research?
PubChem users have frequently expressed interest in having a downloadable, schema-less database. PubChemRDF enables the NoSQL database access and query of PubChem databases. Using PubChemRDF, one can download the desired RDF formatted data files from the PubChem FTP site, import them into a triplestore, and query using a SPARQL query interface. There are a number of open-source or commercial triplestores, such as Apache Jena TDB and OpenLink Virtuoso (a list of triplestores can be found here: http://en.wikipedia.org/wiki/Triplestore).
Other than triplestores, PubChemRDF data can also be loaded into RDF-aware graph databases such as Neo4j, and the graph traversal algorithms can be used to query the RDF graphs. At last but not least, the ontological representation of PubChem knowledge base allows logical inference, such as forward/backward chaining.
The RDF data on the PubChem FTP site is arranged in such a way that you only need to download the type of information in which you are interested, so you can avoid downloading parts of PubChem data you will not use. For example, if you are just interested in computed chemical properties, you only need to download PubChemRDF data in compound descriptor subdomain. In addition to bulk download, PubChemRDF also provides programmatic data access through REST-full interface.
Where can you learn more about this?
To get an overview of the PubChemRDF project, please view this presentation. To learn more about detailed aspects of PubChemRDF and how to use it, please view this presentation. The PubChemRDF Release Notes provide additional technical information about the project.
Additional blog posts will follow on PubChemRDF project topics, including: the FTP site layout, the REST-full interface, and ways to utilize PubChemRDF for research purposes including using SPARQL queries.
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Wednesday, January 29, 2014
Extending Fermat to Other Powers
January 29'th, David Strumfels, A Medley of Potpourri blog
We all know Fermat's famous Last Theorem, solved almost 20 years ago (!) by Andrew Wiles (using mathematical techniques the Fermat did not have, so his proof remains a mystery to history). The theorem states that no three positive integers a, b, and c can satisfy the equation an + bn = cn for any integer value of n greater than two. Examples: 3^2 + 4^2 = 5^2, and 12^2 + 5^2 = 13^2.
I'd been toying around with variations of combining various integers raised to various powers for some time (when you enjoy doing something you don't notice how much time), when I observed that:
3^3 + 4^3 + 5^3 = 6^3. In other words, here I had found (undoubtedly not for the first time in history) a group of four positive integers, a, b, and c, can satisfy the equation a^n + b^n + c^n = d^n whenever n = three.
But does Fermat's modified Theorem apply here too? Can n never exceed three? Could a similar method be used to prove this Theorem? And furthermore, does the fact of squares and cubes having these relationships, mean they keep on going up the line, infinitely. E.g., can five integers, raised to the fourth power, be found with this relationship? And on and on? (The 5/4 set is false for 2,3,4,5,6, if you are curious; try it.)
Now I am no mathematician, but a little math instinct tells me something interesting is going on here. A very large theorem, encompassing Fermat's and our third power analogue and possibly beyond feels ... well, like a genuine mathematical conjecture at least, if I use the word correctly. First, I shall look for a fourth power analogue, for if it doesn't exist then I am blowing smoke (I have to assume it will be found, if at all, with fairly small integers, as with the second and third powers.)
I will work on this, and feel free to give it your all too, if you want to. That's all for now.
David J. Strumfels
Abuse of Statistics in Obscuring ~2000-2013 Warming Plateau
Asteroid Initiatives @AsteroidEnergy 12m
RT @EarthVitalSigns 2013 global surface temp tied for 7th warmest year on record http://1.usa.gov/Mg6Pe7 #NASA pic.twitter.com/aygxwowGA0
RT @EarthVitalSigns 2013 global surface temp tied for 7th warmest year on record http://1.usa.gov/Mg6Pe7 #NASA pic.twitter.com/aygxwowGA0
First Weather Map of Brown Dwarf
ESO’s VLT charts surface of nearest brown dwarf
29 January 2014
Notes
More information
Links
Contacts
Max Planck Institute for Astronomy
Heidelberg, Germany
Tel: +49 6221 528 406
Email: ianc@mpia.de
ESO Public Information Officer
Garching bei München, Germany
Tel: +49 89 3200 6655
Cell: +49 151 1537 3591
Email: rhook@eso.org
Is Industrial Hemp The Ultimate Energy Crop?
By Thomas Prade, Swedish University of Agricultural Sciences
Bioenergy is currently the fastest growing source of renewable energy. Cultivating energy crops on arable land can decrease dependency on depleting fossil resources and it can mitigate climate change.
But some biofuel crops have bad environmental effects: they use too much water, displace people and create more emissions than they save. This has led to a demand for high-yielding energy crops with low environmental impact. Industrial hemp is said to be just that.
Enthusiasts have been promoting the use of industrial hemp for producing bioenergy for a long time now. With its potentially high biomass yield and its suitability to fit into existing crop rotations, hemp could not only complement but exceed other available energy crops.
Hemp, Cannabis sativa, originates from western Asia and India and from there spread around the globe. For centuries, fibres were used to make ropes, sails, cloth and paper, while the seeds were used for protein-rich food and feed. Interest in hemp declined when other fibres such as sisal and jute replaced hemp in the 19th century.
Abuse of hemp as a drug led to the prohibition of its cultivation by the United Nations in 1961. When prohibition was revoked in the 1990s in the European Union, Canada and later in Australia, industrially used hemp emerged again.
This time, the car industry’s interest in light, natural fibre promoted its use. For such industrial use, modern varieties with insignificant content of psychoactive compounds are grown. Nonetheless, industrial hemp cultivation is still prohibited in some industrialised countries like Norway and the USA.
Energy use of industrial hemp is today very limited. There are few countries in which hemp has been commercialised as an energy crop. Sweden is one, and has a small commercial production of hemp briquettes. Hemp briquettes are more expensive than wood-based briquettes, but sell reasonably well on regional markets.
Large-scale energy uses of hemp have also been suggested.
Biogas production from hemp could compete with production from maize, especially in cold climate regions such as Northern Europe and Canada. Ethanol production is possible from the whole hemp plant, and biodiesel can be produced from the oil pressed from hemp seeds. Biodiesel production from hemp seed oil has been shown to overall have a much lower environmental impact than fossil diesel.
Indeed, the environmental benefits of hemp have been praised highly, since hemp cultivation requires very limited amounts of pesticide. Few insect pests are known to exist in hemp crops and fungal diseases are rare.
Since hemp plants shade the ground quickly after sowing, they can outgrow weeds, a trait interesting especially for organic farmers. Still, a weed-free seedbed is required. And without nitrogen fertilisation hemp won´t grow as vigorously as is often suggested.
So, as with any other crop, it takes good agricultural practice to grow hemp right.
Being an annual crop, hemp functions very well in crop rotations. Here it may function as a break crop, reducing the occurance of pests, particularly in cereal production. Farmers interested in cultivating energy crops are often hesitant about tying fields into the production of perennial energy crops such as willow. Due to the high self-tolerance of hemp, cultivation over two to three years in the same field does not lead to significant biomass yield losses.
Small-scale production of hemp briquettes has also proven economically feasible. However, using whole-crop hemp (or any other crop) for energy production is not the overall solution.
Before producing energy from the residues it is certainly more environmentally friendly to use fibres, oils or other compounds of hemp. Even energy in the fibre products can be used when the products become waste.
Recycling plant nutrients to the field, such as in biogas residue, can contribute to lower greenhouse gas emissions from crop production.
Sustainable bioenergy production is not easy, and a diversity of crops will be needed. Industrial hemp is not the ultimate energy crop. Still, if cultivated on good soil with decent fertilisation, hemp can certainly be an environmentally sound crop for bioenergy production and for other industrial uses as well.
Thomas Prade receives funding from the Swedish Farmers’ Foundation for Agricultural Research, the EU commission, the Skåne Regional Council and Partnership Alnarp.
This article was originally published at The Conversation.
Read the original article.
Monday, January 27, 2014
Study examines the development of children’s prelife reasoning
Boston University / January 28, 2014 / Cognition
Most people, regardless of race, religion or culture, believe they are immortal. That is, people believe that part of themselves–some indelible core, soul or essence–will transcend the body’s death and live forever. But what is this essence? Why do we believe it survives? And why is this belief so unshakable?
A new Boston University study led by postdoctoral fellow Natalie Emmons and published in the January 16, 2014 online edition of Child Development sheds light on these profound questions by examining children’s ideas about “prelife,” the time before conception. By interviewing 283 children from two distinct cultures in Ecuador, Emmons’s research suggests that our bias toward immortality is a part of human intuition that naturally emerges early in life. And the part of us that is eternal, we believe, is not our skills or ability to reason, but rather our hopes, desires and emotions. We are, in fact, what we feel.
Emmons’ study fits into a growing body of work examining the cognitive roots of religion. Although religion is a dominant force across cultures, science has made little headway in examining whether religious belief–such as the human tendency to believe in a creator–may actually be hard-wired into our brains.
“This work shows that it’s possible for science to study religious belief,” said Deborah Kelemen, an Associate Professor of Psychology at Boston University and co-author of the paper. “At the same time, it helps us understand some universal aspects of human cognition and the structure of the mind.”
Most studies on immortality or “eternalist” beliefs have focused on people’s views of the afterlife. Studies have found that both children and adults believe that bodily needs, such as hunger and thirst, end when people die, but mental capacities, such as thinking or feeling sad, continue in some form.
But these afterlife studies leave one critical question unanswered: where do these beliefs come from? Researchers have long suspected that people develop ideas about the afterlife through cultural exposure, like television or movies, or through religious instruction. But perhaps, thought Emmons, these ideas of immortality actually emerge from our intuition. Just as children learn to talk without formal instruction, maybe they also intuit that part of their mind could exist apart from their body.
Emmons tackled this question by focusing on “prelife,” the period before conception, since few cultures have beliefs or views on the subject. “By focusing on prelife, we could see if culture causes these beliefs to appear, or if they appear spontaneously,” said Emmons.
“I think it’s a brilliant idea,” said Paul Bloom, a Professor of Psychology and Cognitive Science at Yale who was not involved with the study. “One persistent belief is that children learn these ideas through school or church. That’s what makes the prelife research so cool. It’s a very clever way to get at children’s beliefs on a topic where they aren’t given answers ahead of time.”
Emmons interviewed children from an indigenous Shuar village in the Amazon Basin of Ecuador. She chose the group because they have no cultural prelife beliefs, and she suspected that indigenous children, who have regular exposure to birth and death through hunting and farming, would have a more rational, biologically-based view of the time before they were conceived. For comparison, she also interviewed children from an urban area near Quito, Ecuador. Most of the urban children were Roman Catholic, a religion that teaches that life begins only at conception. If cultural influences were paramount, reasoned Emmons, both urban and indigenous children should reject the idea of life before birth.
Emmons showed the children drawings of a baby, a young woman, and the same woman while pregnant, then asked a series of questions about the child’s abilities, thoughts and emotions during each period: as babies, in the womb, and before conception.
The results were surprising. Both groups gave remarkably similar answers, despite their radically different cultures. The children reasoned that their bodies didn’t exist before birth, and that they didn’t have the ability to think or remember. However, both groups also said that their emotions and desires existed before they were born. For example, while children generally reported that they didn’t have eyes and couldn’t see things before birth, they often reported being happy that they would soon meet their mother, or sad that they were apart from their family.
“They didn’t even realize they were contradicting themselves,” said Emmons. “Even kids who had biological knowledge about reproduction still seemed to think that they had existed in some sort of eternal form. And that form really seemed to be about emotions and desires.”
Why would humans have evolved this seemingly universal belief in the eternal existence of our emotions? Emmons said that this human trait might be a by-product of our highly developed social reasoning. “We’re really good at figuring out what people are thinking, what their emotions are, what their desires are,” she said. We tend to see people as the sum of their mental states, and desires and emotions may be particularly helpful when predicting their behavior. Because this ability is so useful and so powerful, it flows over into other parts of our thinking. We sometimes see connections where potentially none exist, we hope there’s a master plan for the universe, we see purpose when there is none, and we imagine that a soul survives without a body.
These ideas, while nonscientific, are natural and deep-seated. “I study these things for a living but even find myself defaulting to them. I know that my mind is a product of my brain but I still like to think of myself as something independent of my body,” said Emmons.
“We have the ability to reflect and reason scientifically, and we have the ability to reason based on our gut and intuition,” she added. “And depending on the situation, one may be more useful than the other.”
Most people, regardless of race, religion or culture, believe they are immortal. That is, people believe that part of themselves–some indelible core, soul or essence–will transcend the body’s death and live forever. But what is this essence? Why do we believe it survives? And why is this belief so unshakable?
A new Boston University study led by postdoctoral fellow Natalie Emmons and published in the January 16, 2014 online edition of Child Development sheds light on these profound questions by examining children’s ideas about “prelife,” the time before conception. By interviewing 283 children from two distinct cultures in Ecuador, Emmons’s research suggests that our bias toward immortality is a part of human intuition that naturally emerges early in life. And the part of us that is eternal, we believe, is not our skills or ability to reason, but rather our hopes, desires and emotions. We are, in fact, what we feel.
Emmons’ study fits into a growing body of work examining the cognitive roots of religion. Although religion is a dominant force across cultures, science has made little headway in examining whether religious belief–such as the human tendency to believe in a creator–may actually be hard-wired into our brains.
“This work shows that it’s possible for science to study religious belief,” said Deborah Kelemen, an Associate Professor of Psychology at Boston University and co-author of the paper. “At the same time, it helps us understand some universal aspects of human cognition and the structure of the mind.”
Most studies on immortality or “eternalist” beliefs have focused on people’s views of the afterlife. Studies have found that both children and adults believe that bodily needs, such as hunger and thirst, end when people die, but mental capacities, such as thinking or feeling sad, continue in some form.
But these afterlife studies leave one critical question unanswered: where do these beliefs come from? Researchers have long suspected that people develop ideas about the afterlife through cultural exposure, like television or movies, or through religious instruction. But perhaps, thought Emmons, these ideas of immortality actually emerge from our intuition. Just as children learn to talk without formal instruction, maybe they also intuit that part of their mind could exist apart from their body.
Emmons tackled this question by focusing on “prelife,” the period before conception, since few cultures have beliefs or views on the subject. “By focusing on prelife, we could see if culture causes these beliefs to appear, or if they appear spontaneously,” said Emmons.
“I think it’s a brilliant idea,” said Paul Bloom, a Professor of Psychology and Cognitive Science at Yale who was not involved with the study. “One persistent belief is that children learn these ideas through school or church. That’s what makes the prelife research so cool. It’s a very clever way to get at children’s beliefs on a topic where they aren’t given answers ahead of time.”
Emmons interviewed children from an indigenous Shuar village in the Amazon Basin of Ecuador. She chose the group because they have no cultural prelife beliefs, and she suspected that indigenous children, who have regular exposure to birth and death through hunting and farming, would have a more rational, biologically-based view of the time before they were conceived. For comparison, she also interviewed children from an urban area near Quito, Ecuador. Most of the urban children were Roman Catholic, a religion that teaches that life begins only at conception. If cultural influences were paramount, reasoned Emmons, both urban and indigenous children should reject the idea of life before birth.
Emmons showed the children drawings of a baby, a young woman, and the same woman while pregnant, then asked a series of questions about the child’s abilities, thoughts and emotions during each period: as babies, in the womb, and before conception.
The results were surprising. Both groups gave remarkably similar answers, despite their radically different cultures. The children reasoned that their bodies didn’t exist before birth, and that they didn’t have the ability to think or remember. However, both groups also said that their emotions and desires existed before they were born. For example, while children generally reported that they didn’t have eyes and couldn’t see things before birth, they often reported being happy that they would soon meet their mother, or sad that they were apart from their family.
“They didn’t even realize they were contradicting themselves,” said Emmons. “Even kids who had biological knowledge about reproduction still seemed to think that they had existed in some sort of eternal form. And that form really seemed to be about emotions and desires.”
Why would humans have evolved this seemingly universal belief in the eternal existence of our emotions? Emmons said that this human trait might be a by-product of our highly developed social reasoning. “We’re really good at figuring out what people are thinking, what their emotions are, what their desires are,” she said. We tend to see people as the sum of their mental states, and desires and emotions may be particularly helpful when predicting their behavior. Because this ability is so useful and so powerful, it flows over into other parts of our thinking. We sometimes see connections where potentially none exist, we hope there’s a master plan for the universe, we see purpose when there is none, and we imagine that a soul survives without a body.
These ideas, while nonscientific, are natural and deep-seated. “I study these things for a living but even find myself defaulting to them. I know that my mind is a product of my brain but I still like to think of myself as something independent of my body,” said Emmons.
“We have the ability to reflect and reason scientifically, and we have the ability to reason based on our gut and intuition,” she added. “And depending on the situation, one may be more useful than the other.”
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