Tuesday, June 29, 2010

Indexes and Resources for Science Research

To do science, one has to play the game of science, and that involves a lot of responding to the literature, and a constant contact with new research and trends. One of the great and profound tragedies of college is how few people really know how to do a search and how professors expect students to already have academic research skills. The lack of decent research skills is the single greatest unspoken crisis in higher education. How many college kids have been in college for a very long time and barely know their way around the university library?

How “current” new research has to be depends on the field of science. With Geosciences, for example, materials are useful for longer, and it’s often necessary to view print-paper academic journals more than five years old (nothing short of astonishingly old, at least in scientific terms). For that reason, Geoscientists have perhaps an unfair reputation as conservative, stodgy, and most importantly, late technical adopters, despite the fact they get their journals online through university databases just like everybody else.

With Physics, however, there’s a thriving pre-publishing field where new research materials are shared extensively and informally between colleagues by mail and web abstracts as well as databases for unpublished manuscripts through FirstLook – something absolutely unthinkable in other sciences where placing research online or on a database is pretty much an automatic disqualification from publishing in most scientific peer review journals!

In any case, this is where your university library can be your best friend. In the past, most professors obtained their journals by personal subscription. Now, the majority get their journals from the university library, and the majority get their journals online. The real importance of science and engineering journals is on the online copies; copies of the print journals are(I suspect) just a tacked-on scam just to jack up the price of a journal subscription.

Something I didn’t discover until I was a grad student was how your science librarian is the most useful person in the world. They can cut down your search strategies from 2 or more hours to fifteen minutes. They are nothing short of miracle workers! Especially if they have content area knowledge (my university science librarian has a Masters in Biology).

Databases and indexes are your best tool, and you have to head to your university website to discover which ones they subscribe to and are available. With the crisis-level price gouging by those bloodsucking vampires in academic journals, not all are available; I was nothing short of gobsmacked to see that my college didn’t get (of all the basic reference sources) Encyclopedia Britannica!

As a mathematics undergrad, I eventually became entirely familiar with MathSciNet, an international bibliographic resource of the American Mathematical Society useful for both mathematics and statistics. Likewise, I found “GeoRef,” a database index created by the American Geological Institute, to be totally invaluable for Geoscience References.

There are other subject area databases that should be consulted, and the first one to consult would be “General Science Full Text,” which is typically for students and non-specialists. Other databases for students include the “General Science Index” and “Applied Science and Technology Index.” “Science Full Text Select” includes over 360 journals, and is mostly targeted at high schoolers and community colleges.

Other Databases to discover and consult:

  • “Oceanic Abstracts,” dealing with marine biology;
  • “Zoological Record Plus,” run by the English Zoological Society;
  • “Biological and Agricultural Index Plus,” which is exactly what it sounds like;
  • And last but certainly not least, it’s impossible to even try an academic search without at least consulting H.W. Wilson’s First Search, which sometimes includes full-text, or at least points someone in the right direction.

Finally, one piece of advice: always pay attention to a professor’s curricula vitae, and if possible look them up on “LIS Web of Science,” which tracks academics by name and lists the times their works have been cited. If you’re studying, say, nanodiamond formation and your professor is a foremost expert on the field, he’s going to be pretty miffed and think you’re a shallow researcher if at least you don’t even try to bring up their own work on the topic.

Finally, something has to be said about Wikipedia, the eighth most visited website on the internet. There are some things, like the growth of Wal-Mart esque giant stores and the discussion on why people don’t use public transportation in many cities, where the entire discussion revolves around asking the wrong questions. Few people ask themselves why many people in some cities refuse to use public transportation, and why many people prefer to shop at huge Wal-Mart esque megastores. The answer for both is usually convenience: it’s more convenient for people to not use public transportation, and the huge size of giant megastores means a greater selection – people go to stores because they hope the product they want is available. We can get as sanctimonious as we like, but the truth is convenience is important, and that’s something that critics are disingenuously not acknowledging.

Contrary to the popular belief of many information professionals and snotty librarians, Wikipedia does play a legitimate role in the information infrastructure. If you need the answer to a question fast and RIGHT NOW, Wikipedia can tell you. Want to know the difference between Centipedes and Millipedes? Need a quick look at the Gaussian Integral? Need a fast value for Planck’s Constant? Who was the 25th President of the United States? On what day is Yom Kippur starting in 2011? It’s possible to know these things within five seconds. Not everything requires a Lexis-Nexis search. It’s nothing short of incredible that we live in an age where that’s possible. The ability to know basic facts within five seconds should be the dream of any given information professional.

Sure, writing a paper based on a source that unauthoritative is a dumb idea, since Wikipedia is basically a reference source like an almanac or encyclopedia. However, I’m astounded at Information Professionals and librarians, the single most intransigent profession ever, dedicated to justifying their own existence at a time when it should be one of the most relevant field in our society. In library science, the emphasis is on standardization, something no user really cares about. The resistance to Wikipedia is the most pointless and unproductive fight imaginable. It’s already been lost, as more people use it than any database put together.

Librarians hate change. I have no idea why that statement is even contentious at all. Records for materials are still written in MARC, a code language created in the 1960s. If I’m not mistaken, in the 1960s, dinosaurs ruled the earth. Can you imagine IBM still using a format from the 1960s? What’s more, when library card catalogs were updated to the modern OPAC, they chose to just upload the traditional card catalog online, one of the greatest missed opportunities in the entire history of technology. And how long did it take even very advanced academic OPACs to introduce keyword searching? Images for products? And how many actually have reviews from other users or use Google-style algorithms for determining hit frequency? Many still don’t have these things.

Monday, June 28, 2010

Great video on why there's homosexuality in the world

A few things:

  • The video claims that genetics play a role in gayness, which may be partially true but doesn't tell the whole story. What is considered to be a greater factor is hormonal development inside the womb, which is mentioned later on. Fetuses that develop when the mother is stressed are more likely to be homosexual, something discovered during an analysis of babies that were in the womb during the London Blitz.
  • ...they mention animals are often gay, but there's little mention of how birds are often gay, including (adorably enough) penguins. A current theory in ornithology is that birds "turn gay" as a result of a form of population control. When a population grows too large, some birds turn homosexual.
  • The video really starts getting good at 2:41, where it talks about people that are "fixed." In the opinion of nearly every responsible and reputable psychological organization on the planet, homosexuality is a condition that is not curable. Science has a moral obligation to set the record straight and make people aware of this.
  • Finally, I personally have always been of the opinion that too much is generally made, when explaining homosexuality, about biology instead of culture and definitions. Looking for a biological explanation for why people are gay as opposed to a sociological or psychological one always struck me as pointless, like looking for a biological explanation for something like politeness. What etiquette is differs from society to society, so how can there be an etiquette gene, anyway? Here's a dirty little secret about psychology: a lot of it can't be worked out from applied biochemistry because it's about the interaction of an individual and society. One of the greatest fallacies of modern times is that microphenomena can explain macro-level trends, and sometimes that's true (chemical structure determines properties at larger levels) but most of the time it isn't (crackpot explanations for how genes determine religious practices).


If you break down the composition of the earth's crust element by element, the two most common present in the rocks of the planet are 1) oxygen (locked up into solid molecules, of course) and 2) silicon.

So would it really surprise anyone that the single most common mineral on the crust of the earth is made of silicon and oxygen? Silicon Dioxide...better known as "quartz."

SiO2 is, in addition, the basis for many of the rest of the crystalline minerals, and it has a central role in the field of geochemistry.

Let's take the rest of the most common elements on the earth's crust: sodium, potassium, chlorine, aluminum, magnesium, iron, nickel.

When combined with oxygen, the metals form metallic oxides and non-metallic oxides. When the two types of oxides combine with SiO2, you get two major types of minerals in the earth's crust. When quartz comes together with the non-metallic oxides like potassium oxide, it creates the feldspars, the largest group of minerals on the earth's crust, defined by being light in color. On the other hand, when SiO2 combines with metallic oxide like ferric oxide or ferrous oxide (the difference between the two is an extra atom of oxygen in the valence) you get the ferromagnesian group of minerals.

The importance of quartz doesn't just stop there though. Water is a near-universal solvent and has a great way of breaking things down. The reason that the ocean is salty is because water dissolves the components of most continental rocks, including those made with sodium and chloride...which then proceed to combine in the water as sodium chloride, or sea salt. What happens to the quartz, though? The oxygen is dissolved in water, but the Silicon atom combines again with some others as a result of combining with water to create the various minerals we call the "clay" groups.

All things considered, quartz is pretty busy!

Quartz also has a really extraordinary property: because its crystalline structure is symmetrical it's piezoelectric, which means that it produces an electrical current when pressure is applied and the shape of the crystal is changed - or alternatively, the shape of the crystal changes when electricity is applied. This is because as it is perfectly symmetrical, it is impossible to separate its changes from pressure. Crystals can exist in one of 32 different forms - 20 of which are non-symmetrical, and quartz lucked out in that it can work this way.

Quartz crystals are generally useful when it's necessary to change energy from one form to another. Microphones turn sound to electrical energy. Though quartz was the first piezoelectric material discovered, it's barely used for that purpose these days: materials with large crystals are common like ceramic oxides (which are usually crystals of things like aluminum oxide).

Crystals are often used to power gadgets in science fiction like laser beams, but their greatest utility is in sound alteration: as quartz crystals work better at high frequencies, they're better at ultrasonics than normal sound waves.

Lord Kelvin's less famous brother Jimmy

What I find amazing about James Thomson is that he was no shoe salesman, yet he was totally overshadowed by his older brother William...a guy you might have heard of by the name of Lord Kelvin.

Lord Kelvin's less famous brother Jimmy was the president of the Scottish Society of Shipbuilders and Engineers from 1884-1886. He was a true scientific Renaissance man, who did research into glacier motion and the flow of rivers, and who also invented a type of accelerated turbine used for underwater vehicles. He was also the first person to invent the term "interface," a word to this day. He was the closest thing in reality to one of those TV scientists like Dr. Benton Quest that can do Nuclear Physics one day and anthropology and linguistics the next.

James Thomson's best contributions by far were to the field of mathematics. Based on the work of the Bavarian engineer J.H. Hermann, Jimmy created an improved version of the polar planimeter - an instrument that allows area to be determined on a flat surface of any arbitrary and irregular shape.

What's more, he was the first to coin the term "radian" for the single most useful angle of measurement in calculus, the length of an arc of a sliced of subtended angle that is equal to the radius of a circle. Radians are useful because they allow derivative and integral identities to be expressed in very short time-saving terms. What's more, in trigonometry, the relationship between sine and cosine angles can only really be expressed in radians and it's extremely awkward to represent in any other way.

Among other things, radians are useful in determining the speed of rotation (something physicists call angular velocity). The radian is also used in (God help us) Quantum Mechanics, where it is necessary to describe the functions of Planck's Constant. According to Max Planck, the flow of energy is determined by fundamental "bits" in the universe, Quantum. Energy can't assume any given variable range, but only on a finite set of ranges determined by grouping Quanta. It's possible to make something move a "little bit faster" or making something "a little bit brighter" because the amount of Quanta involved are very, very tiny so they're invisible to the everyday scale. Planck's Constant is used to describe the scale of quanta as the smallest amount of energy a quanta can have, and it is necessary to use radians to understand it because when applying Planck's constant to energy, you need to figure out the relationship between quanta and frequency, which comes in waves as in trigonometry.

This was the guy that was Lord Kelvin's "less famous" brother! Amazing! Why would a guy like this be known as the lesser of the two brothers, anyway?

Because Lord Kelvin did nothing short of create the unifying principles of physics, almost like Darwin created the unifying principles of the biological sciences. He codified the Laws of Thermodynamics, and connected how heat functioned in a way similar to that of electric charges, a unifying idea that was one of the most crucial in the history of science. Though Faraday discovered that electromagnetism needs a medium to flow, it was Lord Kelvin that put forth the mathematical models for how that could be. It was also Lord Kelvin who speculated on the idea of a possible "absolute zero," and the idea that heat is actually a form of motion.

All that said, why is it that Lord Kelvin is better remembered than his engineer brother? Scientists are often called impractical Ivory Tower people, especially in the face of "doers" like engineers and industrial scientists. Scientists that work with "theory" (a term misunderstood by people outside of science) are viewed as less crucial to the world than inventors and practical people. Alas, in the end, it is the theorists that end up being ultimately more important because theories in science are not half-baked guesses, but grand, unifying ideas that explain facts and make predictions. More is ultimately learned, and more ultimately comes out of a theory. Lord Kelvin tried his hand at being an engineer, too, like his famous brother, but more people remember his formulation of the laws of thermodynamics than his efforts at telegraphing and his building a newer and better galvanometer.

Sunday, June 13, 2010

Why is there so much marble in Vermont, anyway?

The other day, I got a chance to use those credits in Geoscience. Never underestimate how useful any knowledge can be.

My sister-in-law was talking about buying marble countertops, purchased from Vermont. This should tell you something about my sister-in-law right there, a woman that prides herself on all the cliches of upper middle class McMansion ownership - you can take the girl out of Jersey, but...!

And she wistfully wondered, rhetorically if not expecting an answer, why there is so much marble in Vermont anyway.

Lucky for her I did a ton of projects on the stratigraphy and history of New England, so to her astonishment there actually is an answer.

Here it is in a nutshell:

Marble is a metamorphic carbonate rock, which means it was originally one type of rock that became another. Take some underwater sedimentary deposits, like limestone, which is mostly CaCO3, and is extremely water-soluble,. Now, as limestone was deposited by sedimentary action on the ancient continetal shelf, a range of volcanic mountains came close and the heat and pressure forced the limestone to crystallize. Because limestone contains various other materials inside it, these impurities form the distinctive coloring and swirls that add to marble's distinctive look.

This all happened during an event in the Cambrian, called the Taconic Mountain Building Event, around 500-470 million years ago, when New England formed because of the closing of a shallow sea lined with volcanic islands....the two ingredients to create marble deposits. There are even some limestone deposits that weren't sufficiently metamorphosed and didn't crystallize, and remain carbonate rocks.

By the way, the Taconic Mountains I'm describing here no longer exist anymore and have nothing to do with the modern-day Taconic Mountains; we only know of their former existence through geologic clues. The modern-day Taconic Mountains actually pushed up the tip of the old, worn-down ancient Taconics.

For a little bit of perspective on how huge a scale geologic time operates, 500-470 million years ago, there was absolutely zero land-life, mostly because the atmospheric composition of the atmosphere was such that anything that tried to live on land would have been cooked by ultraviolet rays. Likewise, at this point in history, there were no creatures with a backbone that would be the ancestors of vertebrates, except at the very end. The Ordovician, which comes at the tail end of this development, is also called "the Age of Fishes."

This is actually not that huge compared to some other mineral deposits. Heck, Minnesota's state gem, the Lake Superior Agate, on average formed about a billion years ago!

(The process of mountain-building is called Orogeny. If you want to do Geology, you gotta speak the lingo. For my fellow lovers of Greek myth and culture, Oreads are the rarely-seen Mountain Nymphs, which has the same root. It goes to show how a little Greek never hurt anybody!)

Usually, I try to have some moral here, something we can learn that's bigger than just the science, and I guess it's this: part of intellectual curiosity means never assuming a question is unanswerable. My sister-in-law probably didn't appreciate me being pushy and volunteering this information, but the point is an answer existed for the question that she had.