Category Archives: Science

Some Cool Science Sites

Whether you like it or not, science holds a central and critical role in modern society. Even those of us who are science-adverse still have the cell phone, the car, and the TV that are the direct result of scientific innovation. But, beyond that, science has transformed how we view the universe, as well as how we view our place within it. It behooves all of us to know at least a little bit about science so that we can better understand the world in which we live. Here are a few science related sites I stumbled upon that are worth the visit.

The American Institute of Physics, publisher of Physics Today, also runs the Center for History of Physics. Their mission (from their website):

AIP’s Center for History of Physics works to to preserve and make known the historical record of modern physics and allied sciences. Through documentation, archival collections and educational initiatives, the Center ensures that the heritage of modern physics is safeguarded and its story accurately told.

One of the exhibits in the Center is Cosmic Journey: A History of Scientific Cosmology. This exhibit traces the development of human understanding and views of the universe in which we live, from the beginnings of a scientific approach to looking at the universe of the Greeks to the most recent tools scientists are using today to examine the mysteries of the universe. They also have exhibits on Marie Curie, Albert Einstein, the transistor, Heisenberg and uncertainty and more.

Game theory is an up and coming field that tries to bring the rigor of mathematics to human endeavors such as economics, political science and business. Perhaps the most famous game in game theory is the prisoner’s dilemma, as described on the site

A game frequently displayed in television police dramas. Two partners in crime are separated into separate rooms at the police station and given a similar deal. If one implicates the other, he may go free while the other receives a life in prison. If neither implicates the other, both are given moderate sentences, and if both implicate the other, the sentences for both are severe.

The role of game theory is to understand what choices people would make in situations like this, if those choices can be predicted, and if those choices are “rational,” or make sense. gives a nice introduction to this field, including interactive games to demonstrate some of the basic principles of game theory.

Mathematics is a broad field with differing levels of applicability to other, more “mundane” disciplines. One example of a branch of mathematics that started off as mathematicians doing math just for the hell of it, but has begun having ramifications for science, is the area of knot theory. For example, knot theory is playing a role in string theory, the supposed successor to quantum field theory and the current best candidate for a Grand Unified Theory of everything. offers an amazing software package, for Mac, Windows and even Linux, for manipulating knots on your computer. In addition to generating pretty pictures (like the one above), you can use the software to examine the topology of knots, such as reducing complex knots to their simplest form (unfolding them). The software is very fun to play with and generates some stunning graphics that would make for an excellent screen saver.

The final site I wanted to mention today is Ben Goldacre’s Bad Science blog. Dr. Goldacre is a doctor and journalist in Britain and he writes a bad science column for The Guardian. His work has appeared in other media as well. In his blog, he discusses the scientific “merits” (or non-merits, more often than not) of reports in the media that claim some scientific legitimacy. He has taken it upon himself to expose bad scientific claims in order to both educate the public about misleading reports as well as to help people learn when scientific claims are not so scientific after all.

The Demon Haunted World by Carl Sagan

Started reading: ~08/01/01
Finished reading: ~09/01/01
Notes written: 10/26/01

I write these notes more than a month after I finished reading the book. I felt it was a very good book, maybe preaching to the choir in my case, but still making a very good case for the need for skepticism, of a need to think rationally about the things that we encounter every day. Sagan recounts many instances of people being fooled by hoaxes, both obvious and not so obvious, of believing them even after the hoax is revealed. People so desperately want to believe something, anything. They don’t look at things rationally, they don’t try to analyze them. They take things at face value, never trying to understand things more deeply than at the level that they are first told.

Sagan makes strong arguements for the need to strengthen scientific education, not only here, but in all parts of the world. People, especially now, now that our world is dominated by the products of science, need to understand that science more. To be able to intelligently interact with their world, they need to understand it better.

Sagan also points out the similarties between the current “fad” of alien sightings and abduction stories and the apparitions of the Virgin in the middle ages. Of how neither have any hard evidence for their occurence, but still are believed at face value. He describes how current knowledge of the workings of the brain do seem to lead credance to the idea of mass delusions. He looks at the witch trials of previous centuries to show how the majority of people can be brought to believe something that is not true, even something that the educated people of the time try to tell them is false.

Sagan does a great job of telling us why we need to learn science, why we need to think skeptically and critically. He also is sympathetic with people and their desire to believe these things. He would be the happiest man in the world if aliens did exist and visit us, but he sees no evidence of such happenings. He knows that people need to believe, need to escape from their world, either because it is mundane, or depressing, or too horrible to deal with. In some ways, it is an interesting comparison with The Amazing Adventures of Kavalier and Clay. There, comic books exist as a doorway to escape. Sagan knows that people need to escape, but he also feels that we need to be careful, that we can’t confuse reality – that which we can test, for which we have evidence – with fantasy. Joe, in The Amazing Adventures of Kavalier and Clay, sees the ability to escape as necessary, as the only thing that has helped him to deal with the events in his life. Sagan, I think, doesn’t feel this is bad, just that people need to be able to tell the fantasies of their escape from the reality around them. And, the key way to be able to do this is to know more about science, as a window to understanding reality, as a tool for doing so.

I agree completely with everything Sagan says. I may not be quite as wanting to find aliens or these things, but I am wanting the fantastic to be real. I would like to see ghosts and have these other shades of existence be real. But, as Sagan, I don’t see any evidence for these things. I think that we all need to be a bit more of a scientist, that we need to be able to tell reality from fantasy just a bit more than most of us are able to. I think that many of us are easily swayed and confused by stories of the fantastic, that we so desperately want to believe in something that lets us escape our mundane lives, our lives too horrible to deal with, that we latch on to anything that comes along. We are, in some real sense, sheep, that would rather be told what to believe than to try to investigate the world and learn how it is for ourselves. This isn’t true just of the nature of reality, but also in every realm of human existence. We are told by our governments what to believe about the enemy, we don’t think for ourselves. Blind patriotism plays the same role here as blind faith in religion. We don’t think for ourselves, we just believe the status quo given to us by those in power. Sagan wants us all to be a bit more scientific so we can also deal with these kinds of fantasies as well.

Is God the Answer?

Anthony Gottlieb has a very interesting article on the New Yorker website.  His article, Atheists with Attitude, is about the recent “flood” of books that defend an atheist view of the world, some being fairly hostile to religion.  (I tried to begin Richard Dawkin’s book The Selfish Gene, which is one of his most famous books, and had a hard time getting past his hostile attitude, even though I’m not a very religious person.)

But, it isn’t so much his review of this series of books that I found so interesting.  Rather, it was his paraphrasing of David Hume I found so intriguing:   God is merely the answer that you get if you do not ask enough questions.

When I was younger, I found solice in this view of the world.  Believing in God meant that everything had an answer.  Why does the universe exist?  God created it.  Why are we here?  God put us here.  Why didn’t I get a hit in that game?  God willed it so.  Believing in God meant that there was an answer to every question, every question but one: where did God come from?

I guess that is a question that isn’t supposed to be asked.  But, when I did ask it, I realized that, in not having an answer, it meant I didn’t have a real answer to any of my other questions.  Why does the universe exist?  God created it.  But who created God?  Where did God come from?  In the end, the answer I took so much comfort in didn’t really answer anything for me.

I find that the scientific method is much more fullfilling for me, intellectually and “spiritually”.  I hesitate to use that word, as it isn’t so much a spiritual thing, but rather it just feels better to me.  Science doesn’t have all the answers and there is no scientist that would claim it does.  But, what science does offer is an approach to search for the answers to the questions we pose.  Why does the universe exist?  Well, we don’t know, but science keeps getting a little closer to understanding the earliest moments of the universe.  Why are we here?  It might be just a random bit of luck that life was right on Earth to lead to our existence.  Why didn’t I get a hit in that game?  I just suck at baseball.

Seriously, many more questions go unanswered for me now.  But, I also know that by investigating the questions, I will have a better understanding of the world around me than if I just ascribed everything to God.  I might “know” less than if I relied upon God as the answer for everything, but I definitely understand more.

New papers

I’m on a few new papers that have appeared this year. If anyone reading this is interested in these topics, contact me.

Determining the site preference of trivalent dopants in bixbyite sesquioxides by atomic-scale simulations
by CR Stanek, KJ McClellan, BP Uberuaga, KE Sickafus, MR Levy and RW Grimes
Physical Review B 75, 134101 (2007)

Abstract: Oxides with the bixbyite structure have two crystallographically unique cation sites, namely (in Wyckoff notation) 24d and 8b. Since the symmetries of these two sites are different (C2 and S6, respectively), properties related to solute cations will vary depending on the site preference. Therefore, we have employed atomic scale simulation techniques to systematically investigate the solution site preference of a range of trivalent cations ranging from Sc3+ to La3+ in A2O3 bixbyite oxides (where A ranges from Sc to La). Results reveal that when the solute cation is smaller than the host lattice cation, the 24d site is energetically favorable, but when the solute cation is larger than the host lattice cation, the 8b site is preferred. We also discuss the tendency for solute cations to cluster, as well as corroboration of this work by first principles methods.

Defect kinetics in spinels: Long-time simulations of MgAl2O4, MgGa2O4, and MgIn2O4
by BP Uberuaga, D Bacorisen, R Smith, JA Ball, RW Grimes, AF Voter and KE Sickafus
Physical Review B 75, 104116 (2007)

Abstract: Building upon work in which we examined defect production and stability in spinels, we now turn to defect kinetics. Using temperature accelerated dynamics (TAD), we characterize the kinetics of defects in three spinel oxides: magnesium aluminate MgAl2O4, magnesium gallate MgGa2O4, and magnesium indate MgIn2O4. These materials have varying tendencies to disorder on the cation sublattices. In order to understand chemical composition effects, we first examine defect kinetics in perfectly ordered, or normal, spinels, focusing on point defects on each sublattice. We then examine the role that cation disorder has on defect mobility. Using TAD, we find that disorder creates local environments which strongly trap point defects, effectively reducing their mobility. We explore the consequences of this trapping via kinetic Monte Carlo (KMC) simulations on the oxygen vacancy (VO) in MgGa2O4, finding that VO mobility is directly related to the degree of inversion in the system.

Parallel replica dynamics for driven systems: Derivation and application to strained nanotubes
by BP Uberuaga, SJ Stuart and AF Voter
Physical Review B 75, 014301 (2007)

Abstract: We show that parallel replica dynamics can be extended to driven systems (e.g., systems with time-dependent boundary conditions). Each processor simulates a replica at a driving rate that is M times faster than the desired rate, where M is the number of processors. As in regular parallel replica dynamics, when a transition to a new state is detected on any processor, the times are summed and every processor is restarted in the new state. The state-to-state dynamics are shown to be correct if the processors run at the same speed and the system is driven slowly enough (on each processor) so that the escape rates do not depend on the time history of the drive. We demonstrate the algorithm by stretching a carbon nanotube with a preexisting vacancy, noting a significant dependence of the nature of nanotube yield on the strain rate. In particular, we are able to achieve strain rates slow enough such that the time scale for vacancy diffusion is faster than that for mechanical yield at a temperature of 2000 K. We thus observe vacancy-induced morphological changes in the nanotube structure, providing some insight into previously unexplained experimental features.

Speaking of hypocrisy… the Goracle

Some might infer from my last Rant that I have something against conservatives, singling them out for my vitriol. Well, while I do tend more toward the Democratic side, I don’t think hypocrisy is the sole purvue of the Republicans.

In a recent issue of Time magazine, Charles Krauthammer writes about Al Gore and his campaign to make the world recognize the dangers of global warming. While I believe that this is an important campaign and that we, the global we, must do something about it, Krauthammer makes a number of good points about Gore’s approach, some of which I’d had issues with myself.

The basic problem with Gore (or as Krauthammer calls him, the Goracle) and his message is that he doesn’t practice what he preaches. His mansion in Tennessee consumes 20 times as much power as the average home in the US. That is, of course, enough to power 20 of Gore’s neighbors (well, probably not Gore’s neighbors, but still). And yet, Gore is “carbon neutral”. He gets this status by purchasing carbon credits, which means that he pays to have some other place reduce their carbon emissions by either reducing their amount of pollution or planting the corresponding number of trees to soak up the equivalent amount of carbon dioxide. Usually, these “other places” are third world countries.

I’ve had issues with the idea of “carbon credits” since I first heard of them. They don’t solve the problem of global warming. If we don’t have caps, carbon credits may lead to more trees being planted in Africa, but it doesn’t stop the construction of new coal burning plants next door to the newly planted trees — the overall carbon emissions don’t necessarily decrease and may just as likely go up. If we do have caps, eventually the rich countries will buy all of the carbon emission rights, leaving none for the poor countries who are then unable to develop their economies. This may seem to be not much of a problem for the rich countries, but it would exacerbate resentment of poor countries towards rich countries and problems like illegal immigration. If the overall goal is to get all of the world’s countries to roughly the same standard of living, carbon credits with caps is definitely not the way to go.

To solve the problems of global warming will take a dramatic shift in how we live. It is impossible, at this time, to imagine our lives without any carbon emissions, and I don’t think I or any sensible person is advocating that. But, it will require that we change how we live.

I don’t claim to have done much in this area myself. I try to do the little things: I carpool to work, removing two cars off the road; my wife Lisa and I bought a relatively fuel-efficient car (a Ford Focus); we don’t have multiple TVs blaring at the same time (though during football season, I do have a second one going to watch the games); we have a high-efficiency washer and dryer. But, these aren’t radical steps.

However, I’m not claiming to be carbon neutral. This is the problem I have with Gore. While I believe in his message, that we need to do something now to solve global warming, I don’t believe in the messenger. When his idea of being carbon neutral isn’t to change how he lives but to buy carbon credits, he loses all credibility with me. And I’m on his side! How does the other side, the ones that are skeptical of global warming, view him and his message?

The average person cannot afford to do what Gore is doing. For Gore, paying for some carbon credits is no big deal as he has the wealth to afford it. So does most of Hollywood, who lavished him with so much praise recently. The average American cannot afford these credits. So, even in the US, eventually you will have the rich who can pollute all they want while the poor are effectively paying for it by having to make the changes in their lives to compensate. And by poor, I mean in a relative sense; the middle class will have to pay.

No one likes a messenger who doesn’t live by his message. How well would Jesus’ message had been received if, while accosting the money lenders in the temple, he was a leader of a crime gang? If the Apostles were out roughing people up in the streets for money? Jesus’ message, Ghandi’s message, Martin Luther King’s message, all gathered strong adherents and admirers because there is a sense that they lived their message. They didn’t just preach their message, they were their message.

If Gore is going to convince the vast majority of Americans that global warming is serious and serious steps need to be made to curtail it, he needs to change the way he lives. Otherwise, he will always be a target for his critics who just write him off as a hypocrit.