My Chemical Journey

Introducing Chemistry for Cowards

2011-02-07T21:26:00.001-05:00

While the purpose of this blog has always been to trace my own progress in learning about chemistry, I find myself more and more interested in field of chemical education. I become more interested in why it is more people don't understand chemistry every time I hear someone make an egregious error, like identifying "negative ions" as some kind of insidious miasma that must be purged from the air. Other times people will fail to understand something as basic as the idea that water is water, no matter where it comes from, one molecule of water is that same as any other molecule of water. So I've spent a lot of time considering what would be necessary in a primer for chemistry. Not another general chemistry textbook, just something that will give people enough basic knowledge that they could open up such a textbook and follow along pretty much anywhere.

I realize there will always be people who will never care enough about chemistry to read through a single post, no matter how well-written, on chemistry. So instead of trying to accomplish the impossible task of teaching the uninterested chemistry, I'm going to try and explain it to people who have at the very least a passing interest, and possibly, an intense fear. There are any number of people who have thought to themselves, "Oh, I'd love to learn about chemistry, but I'm not risking my GPA/graduation by taking up the subject just because I'm curious!" I might add: Pshaw on the society that punishes curiosity!

So I want to announce the beginning of a series of posts on the subject called, "Chemistry for Cowards: Everything you wanted to know about chemistry, but were afraid to ask." These posts will differ from other explanatory posts in that they will not be about specific phenomena, but be a way for people to sink their teeth into more fundamental topics. The specific goals here are to allow a person to follow a teenager's general chemistry homework with a certain amount of confidence. The next goal will be to allow the reader to use the following terms with limited confidence (the only form of confidence that ever means anything):

Atom
Molecule
Ion
Electron
Proton
Nuetron
Isotope
Heavy water
Nuclear
Nuclear Reactor
Control rod
Element
Periodicity
Hydrocarbon
Organic
Thermodynamics
Ideal Gas
Acid
Mole
Stoichiometry
Base
pH
Solubility
Chemical formula

The list of terms is minimal but not all inclusive. It's important for me to point out that this is chemistry for cowards. This isn't chemistry for autodidacts. If you find these posts disappointingly basic, that's because they're designed to be one notch below an introductory college text with less math than a high school course. I find people outside of high school are far less willing to do math and so I've made the math rather sparse, and in those cases where math is necessary, I explain in detail how the equation works, outlining every step such that there is nothing to fear. I'll also strive to make it easy just to read over the math.

Chemistry purists may object to trying to teach chemistry without math, but I argue I'm not teaching chemistry, I'm introducing it to people. Busy people. People with jobs, who might want to read something interesting on a lunch break without breaking out a pencil and paper. People who read blogs on their phone waiting for the bus. People who may understand these principles, but for whom it's been a while and a quick survey is all they need to jog their memory. People who don't remember how to move a logarithm to the other side of an equation. These people deserve to know about chemistry too.

As I write more posts on the topic, a button will appear in the menu bar, called- what else? Chemistry for Cowards. It will lead to a page that lists posts in the order necessary to understand them. Each post will also have a link back to that page, as well as a list of posts that may be required reading in order to follow along fully. I will strive to make this as user-friendly and easy to follow as possible, without dumbing it down to the point of uselessness. Feedback, as always, is encouraged.

Egypt Link Roundup

2011-02-01T01:03:00.001-05:00

Cartoon released into the public domain by Carlos Latuff

Please submit links and pictures to chemicaljourney@gmail.com

You may also tweet me @superacid.

You will be credited for your submission. Only one person has sent me anything so far. Disappointing since I know people are reading this based on the stats. I'm trying to act as a meatspace-based news aggregator to cut through noise and repetition in the news coming out of Egypt and it just works better if people collaborate. Thanks.

Al-Jazeera English's Live Blog
Wikileak regarding Egyptian military's lack of loyalty to the regime, and preference for "corporate interests."
Wikileak shows Mubarak planned a VP slot for Omar Sulayman since 2005
Google and Twitter team up to help Egyptians tweet through landlines. [Thanks @Jew4Palestine]
Don't Mess with Al-Jazeera
It's not about the Muslim Brotherhood! (The rest of the blog is worth following religiously)
Ramy Raoof's Flickerstream (Since he has been so kind as to license his images with Creative Commons, I will be using them on this blog in future, with attribution of course.)
The End of An Era
Netanyahu warns Egypt could be like Iran.
Omar Sharif voices support for the revolution
Egypt army rules out using force
The Triviality of US Mideast Policy
"Leave already. My hand hurts."
Why Egypt's Government is Stockpiling food


Numerous people (don't know who was first) have pointed out the front page of Asharq Al-Awsat's paper. Saudi-based and government controlled. The headline reads: "...And Mubarak Answered his people's demands" [Not excerpted, ellipses in original]

*The number of times I've published my email address in blogposts, Twitter and elsewhere demonstrates once and for all that it doesn't increase necessarily increase your spam to publish your address in full. Amount of spam to the inbox? Zero. Amount of spam to the junk folder (like I care how much spam it catches)? One more than yesterday. Just sayin'.

What The Hell Is a Scientific Law Anyway?

2011-01-31T21:39:00.004-05:00

In the great evolution wars, I've noticed something get trampled on, misinterpreted, dragged around unceremoniously, and fall to the wayside: The concept of a scientific law. It's almost as if it falls into a nebulous gray area of whatever we want it to be to prove our point. People, generally the more ignorant side of the anti-evolution crowd, will say over and over again, "It's just a theory and not a law." Seemingly unaware that a theory is recognized among scientists to be a very good and evidence-based explanation of a set of phenomena. They use the word theory the way most people do in conversation, to mean "guess". This is something the more educated (but still wrong) anti-evolution people recognize and the honest among them do not perpetuate the argument. Still, they and even the people in the pro-evolution crowd seem to not consistently use the word law to mean what it actually means.

There are two issues at the heart of this. The first is the way common language differs from the way scientists will talk. I told a friend about a simple solution I came up with to a problem I was having, I said I had a hypothesis which I confirmed. He turned to me and sarcastically asked, "Oh really, you had a hypothesis about [trivial problem I can't remember]?" He said this as if I did some grandiose experimentation and analysis. He seemed to argue by implication that a hypothesis is a big thing. Whereas if I had used the word "theory" he wouldn't have objected, that's just how people talk. The word law is subjected to this same abuse, since it seems to imply a definite certainty. In fact, while more informed people know what a hypothesis and a theory is, use of the word "law" isn't really considered carefully.

The other issue is that science has no governing body. There are organizations like IUPAC and the AAS and even the AAAS that attempt in their own big and small ways to bring scientists onto the same page. But certain ideas and concepts aren't always codified, mainly because scientists can do their work well enough without having to sit down and hash out, "Hey, what is a law anyway?" What exactly a law happens to be doesn't impact how scientists work, but is more important as a concept in the philosophy of science.

First, I want to make some things clear, since there are two common misconceptions contributed to in part by, of all things, textbooks. Textbooks will often show the relationship between a law and a theory graphically, which necessitates drawing an arrow from a law or group of laws to a theory. This leads to the idea that:

A) Theories are laws that have been confirmed.

B.)Theories are a set of laws.

Neither of these are true. A law, is in fact a simple observational model of how the world works, minus any explanation. It is, at its core- how the world works, as opposed to why. So a law is often condensed into a simple mathematical statement like:

F=ma

Or,

PV=nRT

These are descriptions of how the natural world seems to work. The first is an equation that defines force, relating it to mass and acceleration. The second is the ideal gas equation that describes the relationship between the pressure, volume, amount, and temperature of an ideal gas using a constant called R. These are immutable facts about the world around us as confirmed by experiment. They are basic models. You might call them equations, but when you discover how these equations can be rearranged and manipulated, you discover that they are in fact- capable of modeling a range of behaviors.

Notice that there is nothing in them that shows how they work. In the force equation, we know that increasing the acceleration of an object increases the force it exerts. From the ideal gas equation we know that lowering the temperature of a gas lowers the volume. But we don't know why the volume changes or the force increases from the equations. We simply know that they do. It's only when we have a theory, something that looks at the various laws and offers some explanation of why they seem to work that we understand the underlying mechanism.

The kinetic theory offers us a cohesive explanation of the ideal gas law. Because the explanation is so general, it offers us an explanation of other things as well, like the Arrenhius equation. It's a bigger model that shows us why the various laws seem to work. Why is force dependent on mass and acceleration? We had to wait for Einstein to really begin to understand that, and quantum electrodynamic theory to start to home in on anything resembling a satisfying answer.

So to go back to evolution: There was never a law of evolution, and the theory of evolution is not some textbook of smaller laws and principles. Instead the theory of evolution explains why a set of smaller models and laws work. It answers the why for instance, of the Hardy-Weinberg equation, it doesn't contain the Hardy-Weinberg equation like a big box.

Laws and theories are only dependent on each other to the extent that they are logically consistent. A good theory, one used by scientists to develop new laws, has proven itself so consistent with other laws and within itself as a framework that new laws and behaviors can be predicted. So evolution already existed as a theory before Hardy-Weinberg was created as a law that showed evolution happening in the natural world. Other times, laws can be pulled together to see whether a theory makes sense. Laws like the ideal gas equation and Arrenhius's equation along with many others have proven conclusively that the phlogiston theory of chemistry could not be true as long as these laws remain valid.

So when a law is in it's infancy, it's appropriate to refer to it as a hypothesis or series of hypotheses. When a theory is in its infancy, it's appropriate to refer to it as a conjecture, or a series of conjectures. Just don't balk when a scientist says hypothesis to mean theory, and conjecture to mean hypothesis. Remember what I said earlier, scientists know what they're talking amongst themselves, so they tend to neglect that the rest of us will be left in the lurch.

So what's the test an average person can use to decide for themselves? Ask for evidence. When a small specific general rule is discovered, and it's confirmed with evidence that it works, it's a law, or part of a law. When a grand explanation isn't contradicted or not at least generally explained by the evidence and the various laws and observations, it's a conjecture.

Evolution is a theory because the laws of genetics, molecular chemistry, mathematics, and statistics underpinning it have been shown to predict behavior in the real world. Within itself, the model evolution posits is largely self-consistent with the evidence so far.

So now I hope the next time you look at a textbook and see arrows and flowcharts demonstrating the process of science, you'll have a better idea of how it really works.

No On HR 3: My Letter

2011-01-31T18:09:00.000-05:00

I've written my congressman, John Lewis, asking him to uphold his commitment to being pro-choice, which I'm glad he is. For those of you who do not know, House bill 3: No Taxpayer Funding for Abortion Act, is a completely fucked up assault on the victims of rape. I can't say better how and why than Sady can, and what follows after the jump is my first draft of the letter I'm sending my congressman, in case you want ideas for how to communicate with your already pro-choice congressperson if you have one. There will be a link to both Sady's post in the sidebar and a resource to find your district representative for as long as it is necessary. I urge you to follow Tiger Beatdown for details as they emerge. In your own letters, please follow the three Ps: Polite, Professional, Persuasive.

The Following is a draft and may contain mistakes and differ from what I ultimately send:

Dear Mr. Lewis,

I'm writing to you about HR 3: No Taxpayer Funding for Abortion Act. As a constituent of your district I'm aware of your strong pro-choice voting record, and applaud it. I hope you will continue to show your support for the rights of women by voting NO on this bill when you get that opportunity. I further urge you to do whatever is in your power to commune with your Democrat brethren who have made the sad choice to sponsor this bill. I would urge you to do whatever you can to attenuate their support, and urge them to consider that the bill has no chance of passing in the Senate, and that it would be a mistake for them to so boldly align themselves with a bill that penalizes the female survivors of rape.

Here is what I also urge you to remind your more misguided fellow party members, and those in the opposition who will listen: In this economy, people in your district and other are having a hard enough time making ends meet. Medical costs can consume a significant part of a person's income, and the only relief some people can find is in the kindness and charity of others. A victim of rape --and I would note that the bill is uses a term that has no meaning and is inherently redundant, “forcible rape”-- or incest is going to be suffering already. To have to bear her rapist's child is to place an unbearable cruelty on her shoulders. While some women have the strength, the fortitude, and the ability to bring such pregnancies to term, we cannot expect this of all women. We cannot expect them to bring a persistent reminder of their own suffering into this world. Since the term “forcible rape” is not one used by law enforcement, it introduces a level of uncertainty and vagueness about what constitutes rape under this oppressive Act and and almost guarantees that victims of rape can be guaranteed not to find exception under this law.

In fact a bill like this is completely unnecessary, since both the Hyde and the Stupak-Pitts amendments. The only purpose this bill serves in both its language and likely intent is to place limitations on the already sparse exceptions. The great tragedy and tremendous injustice of these exceptions is that they specifically target the individuals who are at their most vulnerable: The poorer victims of rape. Not only that, but the term “forcible rape” will likely be construed so narrowly that only the most vicious and violent rapes, the kind that often result in death of the victim, will be considered. The term ignores the fact that all rapes are inherently forcible, for that is the very definition of rape. The violence of a rape is not measurable as a distinct quantity, and the estimations of rough justice is no justice at all for the victims of these crimes. I urge you Mr. Lewis, to do all you can to communicate this to your fellow congresspeople. Even those Republicans who sponsor the bill. I have had success in communicating my take on supposedly “socially divisive” concerns to our Republican Senator Isakson in the past, and am hopeful that at least some across the isle may be able to see the light on this issue.

Sincerely,

[Name]

[Address]

Egypt Update- BREAKING: Cell phone and Internet Shut Down Completely

2011-01-31T16:32:00.001-05:00

I'm getting reports from Ramy Raoof and others that the last Internet connection in Egypt has gone down. Cell phone networks will also be completely closed down.

More details at this post as they come in.

Egypt Link Roundup

2011-01-31T02:31:00.000-05:00

More links on the Egypt situation to come. Submit your own links to chemicaljourney@gmail.com

Tumult in Egypt

2011-01-31T01:02:00.006-05:00

Demonstration at Imbaba in Cairo. Creative Commons photo by Ramy Raoof

The Nile Rises

I've been following the events unfolding in Egypt for a while now. As I write this, there are probably already new developments, and for reasons I'm about to articulate, by the time you read this, (since most of my readership is American and probably tucked in for the night) there may have been massive bloodshed. It's also entirely possible that there will have been no major developments. Such is the uncertainty of the situation. My heart goes out to the people in Egypt, the people on the streets clamoring, shouting at the tops of the lungs for change. I'm with any people trying to overthrow an oppressive dictatorship. Egypt is not only no exception, but it is the Arab dictatorships in particular I hold a special contempt for.

I lived in the Middle East, in and of itself that information does not entitle me to special knowledge or interest. Many a time I've chafed at the pampered expatriate military brat or oil company spawn that claims expertise by simple virtue of the fact that they grew older there. Especially since my experience with such "experts of circumstance" has been that they are heavily sheltered from the realities most of the people living in these countries face. My general rule is that if someone cannot carry a conversation in the language of the country they are discussing, they fall short of the minimum standard for expertise, hands down.

No, I don't claim academic expertise, what I claim is that I deeply give a damn about the outcome. That while not being Egyptian, I desperately want the Egyptian people to succeed in getting a credible democracy because while Tunisia was the spark that ignited this, Egypt will be the key to unlocking a new future for the whole region. People called January 25th, 2011 a day of anger, but if you knew what it was like in Egypt, the poverty, the lack of sanitation, the way basic services were more about lining the pockets of corrupt politicians than fulfilling their roles as a public good you'd know better. You'd know that every day was a day of anger, of frustration, of knowing your lot could be better if it weren't for the meddlesome and capricious nature of living under the dictate of one person and his cronies, and the cronies' cronies.

All across the Middle East, people are subject to governments that don't represent them or their interests adequately. In the Gulf States, the oil wealth has buoyed authoritarian rule by guaranteeing a high standard of living to the citizens of those countries (and really only the citizens- woe betides the Southeast Asian who commits the sin of being a laborer there). But those exceptions prove the rule, since having a foreign-born labor force means malcontents are easily dealt with by deportation. In the other Arab countries malcontents get treated far worse.

Meanwhile, nepotism and the networks of corrupt officials help to separate women from power and their rights in countries just as much as explicit discriminatory laws would in others. A dictator for life must represent the majority and repress and scapegoat the minorities. They enforce their rule with thugs, for whom thuggery proves profitable and reward enough in itself to support the regime. It is my great hope that people in these countries will, for once and for all be able to create open societies that give the breathing room necessary to challenge other oppressions. It's a day I never thought I'd live to see. If we have indeed reached that day.

Graffiti on a military vehicle. Creative Commons Photo by Mona

We may not have reached that day for a number of reasons. There have been reports that indicate the military in Egypt may side with the government. It is entirely possible that these reports -of the military surrounding government buildings- may be accurate while being misinterpreted. It may be the military is simply trying to fulfill a protective role, and sees itself as ensuring that whatever happens, the country does not descend into anarchy. I'm somewhat more pessimistic. The military in Egypt has not traditionally taken sides, but the possibility it may side against the people is not one that I, at this point, can discount. If it does, I anticipate bloodshed. Meanwhile the Egyptian people will grow weary as slowdowns and shutdowns mean that food is becoming scarce and other necessities wear thin. How this plays out not only lies with the disposition of the military. It is clear that the will of the Egyptian people will be tested. But I have faith in them. I hate the trite pathetic generalizations people often make about "quaint" people that border on insulting. Often they marvel at how "sophisticated" people from a certain region are, and pretend that this is anything but a backhanded compliment. I'm not going to do that. I will only say that I have faith in them because they deserve at least that little from me, and from all people. Anyone who fights their own oppression deserves to be given the chance to show that they do not need to be oppressed to be "stable" or "happy" or "prosperous". Indeed, it's common American uncertainty and apprehension over such things that has me retching.

American Apathy, Antipathy, and Uncertainty

The Muslim Brotherhood:

First let us deal with the myth pervading US media at this time. I say it is a myth because only in the media are lazy prognostications presented as fact with a straight-face. There is, I repeat, there is no evidence whatsoever that:

A.) The Muslim Brotherhood plan on taking over.

B.) That they are liable to take over.

C.) That if they did take over, Egypt would descend into absolute theocracy, Taliban style.

Let's take each of these matters separately. First of all, the Muslim Brotherhood has declared that they do not own the revolution. This is not only a statement of fact, but a guarantee in and of itself that they do not own what's happening on the streets. If they did, they could afford to be less shy about it.

As it stands, anyone who knows anything about Egypt knows this about the Muslim Brotherhood: They do not have the popular vote. I think American media likes presenting political situations in other countries as being analogous to American politics, where there are two main parties, and all others are ignored. So everything is heavily dichotomized. Either it's the Muslim Brotherhood, or it's Mubarak. That's not the case at all. Astute Americans and people from other countries know that a lot of countries, Egypt included, use a parliamentary system where there are more than two parties. The diversity in Egyptian political parties ensures that it is unlikely no one will get the plurality of the vote. Would the Muslim Brotherhood gain seats? Yes. Would they have the ability to rule Egypt with an iron fist (assuming they would want to)? No.

Finally, the Muslim Brotherhood is not an equivalent of the Taliban. For one thing, they've shared the experiences of Leftists and moderates they've shared cells with. There's a genuine empathy among the disenfranchised and persecuted that makes them anything but the Taliban, or Al-Qaeda. Al-Qaeda is a paramilitary organization. The Taliban is a Pashtun-dominated Deobantist militia. The Muslim Brotherhood is an opposition political party that publically renounces violence to achieve it's goals and will honor democracy. I can't emphasize enough that here be apples, there be oranges, and waaaaaaaay over there behind the shed tied to a post is a horse. Just because Islam is a common theme throughout, it doesn't make them the same thing. The argument it does is similar to the argument that books have pages, bills have pages and lawsuits have pages, so you don't buy books lest you end up with a lawsuit on your hands- it's completely twisted logic. It only lends credence to the position (which I take) that American media is inherently Islamophobic, and takes for granted that 1.6 billion people manage to live their lives by Islam to differing extents without miraculously all being violent and unpredictable at once. That's what the Muslim Brotherhood is, an extent. I'm no fan of theocratic rule, but I'd take theocratic elements endorsed by the people over despotism and dictatorship any day.

Why American media keeps bringing the Muslim Brotherhood up, despite its eminently non-special role in this is entirely predictable in an environment where the US president only very recently announced that Muslims have a legitimate place in this country.

Israel, and Our Uncritical Support

Let's be honest, talk on Fox News and other networks about Israel in this matter is motivated entirely by a concern for that country that overrides any concern ever shown for democracy in the Middle East. Everyone agrees real democratic reform in the Middle East leads to hostilities against the Israeli state, which has shown unprecedented belligerence for a nation of its size and position. Mainly because we have allowed them to show unprecedented belligerence ever since a US policy shift around the 1967 war. The reason we get mealy-mouthed remarks from Obama and Clinton is due in large part to a realization that if they throw one Arab dictator under the bus, the others are sure to object, and then where, pray tell, would Israel be? The Israelis know better than to brush off what's happening. Right-wing or left-wing, they all see the events unfolding in Egypt and understand the implications. As a side note, where the Saudi and Israeli positions coincide- I'm against them both.

White House photo of Barack Obama talking to Hosni Mubarak.

What's interesting is that US silence and mumbling is in large part due to a bizarre idea of realpolitik. I would argue it's much more realistic and beneficial to US in the long-term over decades to stop propping up dictators and try to make friends with the actual people of foreign nations, it's almost as if the White House (regardless of administration) think that ethical actions are necessarily ineffective and eschew them.

So you see, I'm not a cynic- I just think the people running our foreign policy are incredibly stupid.

Empathy for Adults

One other trend I've noticed, even among many self-proclaimed liberals- is this notion that they shouldn't take sides. Lest it get worse for the Egyptian people. What? Am I hearing this correctly? One group is persecuting another, and you don't want to take sides because the persecuted group might act irresponsibly or act against its own interests in future? That's akin to saying, "Oh, I don't want to be against that pimp, she might spend her money foolishly without him." Am I the only person who sees the furious inanity of that position? Surely I can't be.

This is the difference between viewing the Egyptians as real people with real agency on the one hand, and acting paternalistic and treating them like children on the other. That you are concerned for the future of the Egyptian people is admirable and cute and all, but they have to be treated like adults, and you have to support their right to take risks. Even if they risk their lives. Those lives are theirs to risk. You don't waver on whether an adult should be free just because they might use that freedom to make choices you wouldn't. So you do in fact have to take a side, because this is one of those situations where not taking a side is taking a side. Either you support an undemocratic status quo by default, or you support the right of a people to self-determination. That's something you can do without supporting what they determine.

Others have said their wishy-washy cowardice on the matter is a function of being unsure of who will replace Mubarak. What if the protesters end up with a military dictatorship? So? I fail to understand how siding with the protesters makes either you or them responsible for unexpected outcomes. How does supporting the rights of oppressed people mean that you'd somehow be supporting an unintended consequence of yet another autocracy? At that stage, do you know what you do? You continue to side with the people of Egypt! Do you see how simple that was?

I don't know about you, but I side with this man and that young girl:

I'll let the people on the streets of Egypt have the last word:

الشعب يريد إسقاط النظام

A Brand New Look!

2011-01-29T13:14:00.002-05:00

So I decided that my blog and logo was starting to look a little tired and I made a few adjustments. Let me know what you think. In the meantime, expect me to start making tweaks here and there.

Military Loses Quarter-Teaspoon of VX Nerve Agent

2011-01-28T09:00:00.002-05:00

So this is fun:

Some 1,200 to 1,400 people were locked in the 1,200 sq-mile Dugway Proving Ground for several hours after a vial containing a quarter of a teaspoon of VX nerve agent was reported missing. [BBC]

A complete lock-down was by no means an overreaction. VX nerve gas is extraordinarily lethal. The lethal dose is ~30 μg. To put that in context, according to Wolfram Alpha*, that's about 1,240,000 lethal doses if dispersed effectively. Enough to destroy the city of San Diego. For comparison, Nagasaki and Hiroshima bombings combined resulted in 199,000 casualties (dead and injured.) This sort of thing is dead serious, and it's no surprise that the base went into quarantine until it was found. Of course, I don't want to be alarmist, the chances that this was in the wrong hands or had a chance of being widely dispersed is slim. More likely than not, it was misplaced in a lab, or someone forgot to appropriately log the return or destruction of the specimen. These labs and storage vaults are likely (if reports of biological and chemical weapon labs are to be believed) keep under negative air pressure and from a civil engineering perspective built for containment. It's certainly no joking matter, but the danger in this case was minimal.

So I wanted to take this current event and use it as an opportunity to discuss the role of enzymes. Biochemistry is fascinating, but it's not my favorite kind of chemistry. Still the role of enzymes has always filled me with a certain awe. Enzymes are how nature really does its best chemistry, and so far, we can't really beat enzymes at what they do, though we've managed to harness them using biochemistry and genetics. Think of them as the teeny weeny craftspeople of the lab. They act as catalysts, allowing the human body (or other complex systems) to undertake complex molecular transformations in fractions of a second. If biological systems had to do the sort of slow plodding chemistry that we're used to doing in the lab to complete certain reactions, complex life as we know it could not exist.

First though, a word on catalysis in general. In the non-biological world, there is such a thing as chemical catalysis. However the kind of catalysis chemists do uses rare and/or expensive metals that often act as a surface on which we can mount individual ions and molecules and almost pluck at them like circuit boards. This is a vast oversimplification, catalysts aren't always solid, chemists can't "see" the molecules mounted on the surface, and it's done more than one molecule at a time. Generally though, using catalysts means less energy is needed and fewer steps. Due to the peculiarities of certain molecules, doing something that sounds simple; like attaching two molecules together to form a bigger one, is actually quite complex and can involve multiple steps. Using a catalyst can take down the number of steps required to a handful. Some common candidates for catalysts are titanium, osmium, platinum, palladium, iridium, and gold. Sometimes, they can contaminate a reaction, leading a chemist to believe that a reaction can happen at room temperature, or at impressive rates; when in fact they've just been given false hope, since repeating the experiment won't give the same results.

Whether we're talking about chemical catalysts or enzymes, they have something important in common: They aren't consumed by the reactions they speed up. The same substrate or enzyme molecule can be used over and over again. This is why the catalytic converter in your car, which uses platinum, doesn't require you to replenish the metal every so often. A good thing too, since platinum is very expensive.

Now an enzyme isn't like your basic metal catalyst. They can be huge structures made of multiple proteins called macromolecules. A well known example of a macromolecule (but not an enzyme) is hemoglobin:

Hemoglobin carries oxygen in the bloodstream. It's tremendous, but it only carries one oxygen molecule at a time. Now in the case of nerve function, there's one really important macromolecule that is actually an enzyme:

Okay, so acetylcholinesterase looks more like this. Work with me here.

A common feature in enzymes is the active site. This is where the products come to bind or break down. In keeping with the visual metaphor here, they're AChE's hands. What AChE does is break down acetylcholine, a neurotransmitter. When you want to send a signal to a neuron or muscle, acetylcholine is what tells the neuron to fire, or muscle to contract. There are other neurotransmitters, but acetylcholine is a major one, and we're going to concentrate on it for now. Now of course, you don't want the muscle to stay contracted or the neuron to be perpetually firing, so AChE's very important job is to go in and start breaking down acetylcholine as fast as it can.

Oh, like you've never had a Rhianna song stuck in your head.

Remember how I keep pointing out that enzymes make reactions happen faster at lower energies? Considering you need to be able to fire your muscles and send and receive data quick enough to do a circle-strafe in Halo or swerve to avoid a pothole, AChE needs to be fast, and fast it is. A single molecule of AChE can break down 25,000 molecules of acetylcholine in one second.

Go on. Count 'em. No really, it's a great use of your time.

This is where VX and other nerve agents come in, they do something called allosteric inhibition. You see, enzymes, while truly amazing little beasts, aren't invincible. They often only work in a certain temperature range and pH. But, the one thing that will really shut an enzyme down is allosteric inhibitors. I've made the point before that sometimes how a molecule is shaped is more important than the specific ions or elements in it. Of course, the specific elements are important in reaching the "correct" shape, but it doesn't necessarily mean they're a big part of the main reaction. Allosteric inhibitors, like VX or sarin, latch onto a certain part of the molecule, where they form covalent bonds. It forces the molecule to change shape, including the shape of it's active site. End result? It's a not-so-active site. At this point, it's like a Vulcan nerve pinch. The molecule is out of commission, unable to bind substrates.

"I didn't want to do this AChE, but now I've got that stupid song stuck in my head."

In the human body, the result is death. The nervous system is completely jammed, and since acetylcholine plays an important role in the autonomic nervous system, we're talking about a lot of bodily functions that are extremely necessary but that we do without thinking: Digestion, heartbeat regulation (the heart has its own nerve clusters so it doesn't need the brain to beat, these are affected by the poison directly), breathing. All of that goes into overdrive. This is of course in addition to being unable to control movement, but that's really the least of your worries. Twitching, tightness in the chest, and drooling are early effects of the poison. Treatments usually involve drug cocktails that block acetylcholine receptors, and restore functionality to affected AChE molecules.

Chemical weapons like VX are deadly, effective, and potent. The problem is, like other WMDs they're indiscriminate. Actually, I take that back, they're not indiscriminate- they tend to kill the kinds of people least likely to be wearing masks and suits that protect them from the effects: Non-combatants. This is why the CWC, or *inhales* the Convention on the Prohibition of the Development, Production, Stockpiling and Use of Chemical Weapons and on their Destruction *inhales again* has set a timeline for the destruction of all stockpiles of chemical weapons and munitions. By April 2012, 100% of chemical weapons should be destroyed. Currently, the United States has destroyed ~81%.

What Happened to My Chemical Journey?

2011-01-27T03:39:00.005-05:00

Well, it's been a while since my last post, and a while between my last post and the one before it. I've considered the possibility that the blog could or should be shut down.

When I started this blog, it was because I found myself in a strange phase in my life. I had decided to pursue a life in chemistry, while at the same time being uncertain how much I really wanted to do that. I've always been capricious in my interests and distractions. I didn't know if my choice of chemistry was a whim or a goal at first, primarily because that's the case with everything I start. So, I started a blog where I would discuss chemistry, to remind myself what I liked about the field, to really decide if it was something I wanted to do with my life. I figured, there a billion blogs on the planet, and if I changed my mind and let it fall to the wayside, it would happen quickly and no one would notice. I didn't expect that I would come to a decision so quickly. I developed a passion for the field, a truly unique passion for me, the kind where frustration makes you work harder because the victory is so much sweeter than with other pursuits.

After blogging for a while, I had something of a following. People were reading, I was writing and learning, and everything seemed to be chugging along just fine. However the past year was hard on me, both academically and personally. Mostly personally. The first six months of that year left me truly miserable, and vulnerable. The past six months in particular have been new and unfamiliar, sending me on a bizarre roller coaster ride before spitting me out the other side, somehow with a newly adopted cat named Cicero. Unfortunately, despite that and some other delightful changes, this last year did not treat me well, not in the least. In fact, I've been waylaid. For reasons I really don't want to get into, I'm not studying chemistry anymore. At least not formally. I can, and will return to studying chemistry, but this is a setback. The biggest danger now, if you could call it that, is ending up not going back, not getting back on the path to get where I was going.

I've considered that it's possible I could find myself somewhere better, somewhere that makes me happier than my original goal. But, I don't believe that. The worst of times in my learning about chemistry were still a blast, and the best of times left me feeling immensely satisfied. I like the challenges posed by the field, the way it exercised my mind and left me without real lifelines to any answers that I did not think of myself. I want to get back to it, I want to start out again on the road that I so hesitatingly set foot on with my first post in this blog.

It will take me longer now. I have a lot to do, my biggest current challenge is figuring out how much my mind (which hasn't tackled a single scientific problem in over six months) has retained. It's time to assess the damage as it were. After that, I have to start making up for lost time, to start learning, on my own, in preparation. Both to hit the ground running when I get back to the classroom, and to take this time to get to know things cold, back and forth in detail I did not had time to pursue previously.

This blog, if you're still reading, if you've come back, or if you're new here, will continue. I will write more, and you should watch this space. If anything, it's more useful to me now than it ever was before. In addition to charting my progress, I want to undertake a task I kept putting off since the creation of this blog- the creation of a sort of chemical survey for the uninitiated. A sort of remedial gen chem that could go over the basics from the simplest concepts to introducing, if not explaining the frontiers that those concepts drive outwards. In the beginning, the task of creating this guide and assessing my progress will be almost one and the same. Since I have to see how much chemistry I've forgotten.

I remember reading that when Glenn Seaborg was offered a teaching position after years administering the AEC, he went through the general chemistry textbook used at the university and made sure to answer every problem. Inspired by that, I'll be starting at the very beginning, though I'm sure I'll progress quickly, perhaps quicker than I can write about it, but I'll keep writing the guide nonetheless. After a bad year, it's time for a fresh start. Now what began as a metaphorical title is an absolute tangible reality of this blog. I'm charting my course and logging my progress, as I continue on my chemical journey. It's far from over.

[Comic from XKCD]

Skepticamp Atlanta!

2010-05-20T15:32:00.007-04:00

I attended the annual Atlanta Skepticamp this past weekend. I originally wrote this the day after it ended, but didn't get around to proofreading till today. It's really after the event that I knew what to think of it. When the time came to fill out a brief survey and give feedback, I was a little at a loss to think of anything useful to suggest except, "MOAR SWORDS!" (Explanation to come.) So I'm just trying to pull together a useful description for people thinking of attending in the future. Skepticamp is an event that is set up by any local group of skeptics interested in holding one. It's really just an opportunity for people living in particular locales to gather and present their thoughts and ideas regarding or stemming from skepticism.

First of all, I should point out that this is my first Skepticamp and really my first skeptical event. I wanted to attend the one being held last year, but I wasn't able to due to illness and other assorted life-stupidity. This year, I almost didn't make it again thanks to travel plans which I was able to postpone.

By the time I knew I was going at all, it was too late to set up a presentation, and I'm glad I wasn't given the opportunity, because frankly, I'm an idiot- I'd have tried to. I tend to bite off more than I can chew, and I'd have entertained visions of something way too complicated to pull together in the kind of time I would have actually had. Skepticamp registration is completely open, and anyone can participate, which is part of the appeal. This year's Skepticamp had a theme: Critical Thinking for Everyone.

I participated as best I could, since I signed on to be a volunteer. This mainly involved moving a couple of things around, hanging a Skepchick sign, and helping to clean up at the end- and I use the term "helping" loosely since I mainly stood around looking for something to do that would be useful without getting in the way. The organizers had a good handle on the event. Everything moved on schedule, the equipment (largely) functioned without a hitch and everyone clearly knew what they were doing. I had no idea what to expect, and was suprised, never having been to a skeptical event before (save an informal organizing brunch that turned out to be pleasant enough but entirely superfluous.)

That's my overall impression of the organization. The talks were all good, make no mistake, and I certainly didn't dislike any of them. Certainly there were elements in certain talks I disagreed with, which often had little to do with how interesting they were. Some I simply didn't understand or absorb well enough for my liking. In fact, that's my most serious criticism of the event: That there wasn't always a lot of time to necessarily absorb the presentation, or explain and discuss it. I understand that time is a precious commodity, but often that time was used by speakers more to convey information over implication.

In terms of content of the talks: I don't nitpick as much in real life as I do online, because I have poor memory for details. So the only things that I'll say bothered me were little things that individual presenters would say over and over again, and were somehow obtrusive. One of the most entertaining and vivid presentations was one given by John Clements who is the Director of the Association of Renaissance Martial Arts (The ARMA), where he discussed supernatural and problematic claims made in martial arts. This presenter instantly aroused everyone's interest, including mine, by bringing in swords. I've always loved martial arts, and I took up fencing briefly. My coach had encouraged me to read a few books on the subject, and so I was really interested in the talk from the get-go. He did overly-generalize when discussing Eastern martial arts to some extent. While he is right that the huge emphasis on unarmed combat over armed combat makes for a more dilute set of skills, he did seem to imply that their purpose was largely for combat, or that there was never any rigor.

One of the most popular far-eastern styles in the world come to my mind immediately, [modern] Karate is actually a fairly recent invention that was created for different reasons that would never place it on par with arts of war. Karate as originally concieved was in large part about self-development and discipline and not primarily a combat art. For a while in its early history, even sparring was frowned upon. It's essentially a sport with a distinct philosophy of practice. The expectation was that it would be used for self-defense no more than once in your lifetime, if at all. The more mystical aspects popularly attributed to Karate actually have a lot more to do with bad movies made about it, especially The Karate Kid. Eskrima is an example of an Eastern systematized method of armed combat that relies on angle of attack. I'm not intimately acquainted with every martial art on the planet, but I do know that people have been fighting wars for centuries, and I'm sure that it's an oversimplification to categorize all far-eastern methods of fighting as fitting in a particular mold. However, I do think that he does make some excellent points about how many popular far-eastern styles of fighting are presented to Americans.

The other talk that had a problematic element that stuck in my mind was one where the presenter argued that skeptics should not always be cheerleaders for scientific consensus. I largely agree, and it's certainly a topic worth it's own blog post. What irked me was how he kept mentioning global warming as an instance of scientific consensus we shouldn't necessarily accept. I'm not sure if I rolled my eyes, but I definitely wanted to. He also mentioned that we should paint the global warming "skeptic" with the brush of "holocaust denier" which is a common straw-man. "Denier" means, well- denier. Global warming deniers like George Will are not in any way being compared to people who deny the Holocaust. I'm a little more careful about how I use the term "denier" than some, but I certainly don't hold back because of some purported connection to the phrase, "Holocaust-denier." It simply does not mean that. Never has, never will, and frankly the persecution complex has gotten tiresome. I would also like to point out that cases of scientific consensus being wrong largely involve lack of knowledge about specific phenomena. It's impossible to predict where scientists will be wrong in these cases because it's impossible to know what we don't know we don't know. (You may have to read that a few times for it to make sense.

The presentations I enjoyed the most were the ones like that given by Dr. Ginger Campbell, who runs the Brain Science Podcast. It intrigued me if only because she talked about consciousness and the way neuroscience is in some respects catching up to and outstripping philosophy. I've been very interested in philosophy lately and it just seemed to intersect with my current interests very well. One presentation involved old-wives tales and was a great deal of fun. Another on Wikipedia given by Tim Farley (AKA Krelnik) told me a lot about Wikipedia I already knew, but I also picked up a number of very good ideas, and I found out that the Church of Scientology is banned from editing Wikipedia. The martial arts presentation was also very good, and one of the few that had any significant degree of audience participation. I'd even consider taking the classes his organization offers. I was really hoping he'd use the term "bullshido" and was disappointed when he didn't, but he did describe in accurate detail some unethical practices seen in martial arts demonstrations and learning environments. He really describes a whole wide world of irrationality and trickery that most people don't even think about.

I got the sense social media was supposed to be involved in this event in some vague way, as it is now expected to in almost every human endeavor. Frankly, I'm still waiting for someone to hook their toilet up to Twitter so we get their- um, dispatches. That said, I like social media and I now tweet more actively than I blog. I did a little tweeting on the first day but my phone was too cumbersome to really use effectively. I borrowed my brother's laptop and live-tweeted the shit out of the next day. I would actually think that having the ability to tweet questions would be an interesting development, albeit one that's a challenge to integrate. There was a live stream of the event, and I wanted to try seeing if there were any intriguing questions in the chatroom that I could ask during the Q&A's but I was unable to bring up the chat on the borrowed computer and I didn't have admin access to fix it. (Okay, so maybe I didn't borrow my brother's computer as much as "borrow" my brother's computer- I know, I'm a horrible, horrible person.) Overall, I didn't tweet as much as I would have because it seemed so few others were doing so as well. Either way, it wasn't a significant part of the whole affair, but something I thought I'd mention.

But, and my initial survey didn't reflect this, perhaps the best part of the event was getting to hang out with other skeptics. I took it for granted in the moment, but not a lot of my friends are skeptics and they don't always readily grok certain topics that I'd like to discuss. It's nice to have a conversation about certain ideas where you don't have to lay any ideological railroad tracks for the other person. It was a lot of fun, and everyone was friendly and had a good sense of humor. That's not to say we necessarily discussed skepticism all or even most of the time, but it was nice to have a sounding-board for certain ideas an opinions.

Overall, if you've never been to a Skepticamp, or skeptical event, I highly recommend it. If there isn't an event coming up in your area, the whole point of Skepticamp is that you can start one on your own, wherever you live, with whatever resources you can get your hands on. There are a number of organizations and entities, many of which you'll find in your local area, that are willing to sponsor a group of critical thinkers getting together. To my understanding, the Atlanta Skepticamp started as almost an idle suggestion. I do know that I've been inspired to get more involved with skepticism than I have been lately, and I'm looking forward to possibly giving my own talk at the next Skepticamp.

New Post Over Facts Not Fantasy

2010-02-28T17:17:00.002-05:00

My first, belated post at Facts Not Fantasy.

What? Wait!

2010-02-26T09:29:00.001-05:00

Ever have this sort of thing happen to you: Your flipping through the channels and come across some meh movie you have never seen before and decide to just take the path of least resistance and watch it. It's sci-fi, and therefore full of bad science, but this is okay because you love sci-fi and suspend disbelief...right up until someone starts writing equations on the board.

I had this problem when watching the Fantastic Four (quickie review: watch only if you really have nothing better to do.) I love the Marvel Comics characters and hence the movies, but I skipped out on F4 because it looked like crap- a judgment that turned out to be sound. I'm not one of those people who has a mental block when it comes to movies being inaccurate, but some things do make me chuckle. Before you ask: No the movie wasn't bad because it had some stray hairs scientifically. It was bad because it was bad.

There comes a part where the scientist is working in his immaculate and of course large lab. It is alluded to early on that money is a problem for this man, yet somehow this does nothing to diminish the lab's capacity and capabilities. I'm sure there are underfunded physicists out there who would orgasm at the thought of having that kind of office space. Then again- how much money could he possibly be burning through, looking around it appears that like any good movie scientist, he probably spends most of his time messing around with bright copper sulfate solutions and food coloring in big crystalline flasks.

What he is trying to do is somehow ("somehow" is a magical word in sci-fi) reverse the radiation they experienced and therefore reverse their mutations (cure cancer). Fine, sure thing. He walks over to a board and starts writing... an equilibrium equation. This snapped me out of the storyline instantly. As I once read somewhere, "Math is the ultimate bullshit barrier". For those of you who don't know what an equilibrium constant equation is, it defines the relationship in terms of concentration (and amount) between substances in equilibrium in a system. Now I don't know why this might be necessary, obviously I can't follow an imaginary thought process, but what I find hilarious is the stern look of concentration on his face. Not only is the equation not a particularly mind bending one, but it's utterly trivial. This guy is really chipping away at the problem on step at a time. Geez! If you're going to pull a prop equation out of a physics or chemistry book- at least be in the right section. He should be writing an equation pertaining to radiation or a nuclear reaction up there.

Wakey, Wakey!

2010-02-08T02:02:00.009-05:00

This is slightly stale news, but I haven't really had time to blog on it: The Lancet, the prestigious British Medical Journal that originally published Andrew Wakefield's shall we say, problematic study purportedly linking vaccines to autism, has retracted it [PDF]. I think this is a long time in coming, though I understand why it took so long. Retraction of a peer-reviewed paper is actually a big deal and very uncommon, even for fairly bad papers. Even prestigious journals don't retract papers just because someone turned out to be wrong, or there was a critical error in an experiment that was undertaken in good faith. In these cases it's more typical for the scientists themselves to retract the paper. Usually there has to be very serious issues.

The Big Sin in Wakefield's case wasn't simply being wrong, but in failing to disclose his associations and potential conflicts of interest and not respecting the rights of his research subjects. Reading Autism's False Prophets by Paul Offit, it's actually very clear that Wakefield's research was highly questionable if only because he was working for trial lawyers involved in tort cases against vaccine manufacturers aiming for a class-action lawsuit. For people who argue that pharmaceutical companies have a vested interest in denying vaccine danger, I would like them to consider (however briefly) that Wakefield has had a vested interest in connecting vaccines to some form of disease. This, in addition to the fact that he himself patented a stand-alone measles vaccine, all the while encouraging people not to use the multi-valent vaccine for Measles-Mumps-Rubella (MMR). I should also point out that by contrast, Dr. Offit makes no bones about admitting he works on vaccines himself- a level of disclosure significantly greater than that of Wakefield.

Measles vaccines being grown in chicken eggs. (Photo courtesy of the WHO)

When pharmacuetical companies do research, we know their agenda and scientists can stand back and consider potential biases. The FDA and other government agencies also get involved in monitoring the research and making sure that scientific rigor is being applied. While the FDA has had its debacles, and in all fairness the system is flawed- there is at least some level of openness about the research being done and acknowledgement of who pays the piper, so to speak. With Wakefield, he deliberately withheld his conflicts of interest from the journal, which would have called for increased scrutiny of his research had he done so. That the Lancet published it in the first place was a case of the journal doing it's due diligence with data that seemed plausible from what seemed to be a responsible unconflicted party on the subject. The Lancet would have been manifestly derelict in its duty to inform the medical and scientific communities had it not published such a paper. When it's discovered that the data was bad, the research subjects were mistreated, and that there were significant conflicts of interest- why should the paper stand?

Yet the predictable response of the anti-vaccination movement is talk of "censorship". I remember a day when censorship meant that saying certain things got you imprisoned or killed. In fact, I believe they still do this in some countries and that the people who die speaking freely might have an objection to that characterization. That a publication refuses to publish your drivel isn't censorship- it's discretion. Discretion is an important part of the peer-review process: That people qualified in the field and who understand the state of the science decide its value to others in the community of researchers.

I'm very comfortable calling the anti-vaccination movement anti-science denialists. I'm less comfortable doing that with say- global warming deniers (though I still call them deniers). In the case of people against the idea of anthropogenic global warming, there are those among them who look at the data and come off with at least superficially plausible differing interpretations. Anti-vaccinationists offer no mechanisms of action, do not consider the importance of harm-reduction (even if vaccines did cause autism, the likelihood is so small that vaccination is still worth the risk relative to the risk of infectious disease), they are unmoved by further studies that cannot detect the connection or replicate Wakefield's results, and this is the kicker: IGNORE OTHER POSSIBLE CAUSES FOR AUTISM.

This last one kills me. Dollars that went to confirm Wakefield's results and determine the nature of the purported autism-vaccine link were dollars wasted. That money was money that never went to finding cures or treatments for autism that never worked. People who donated to various anti-vaccine movements have deprived numerous researchers and scientists of funds urgently needed to help those with autism, and if this does turn out to be completely genetic, screening technologies for it. Meanwhile the resulting scare resulted in deaths and disfigurement of numerous children who were not vaccinated because their parents were either misguided or willfully obstinate. People die when you disseminate medical information that happens to be false. When you spread information you know to be wrong- that's simply unconscionable. I sincerely hope Mr. Wakefield finds his mattress small help in falling asleep tonight.

Dirty Word

2010-02-03T12:53:00.003-05:00

Quick! What's the housing of your computer screen made out of? What about the dash of your car?

If you struggled for a moment, I wouldn't be surprised. The first question is ripped directly from the pages of an interesting book I'm reading by Geoff Nunberg of NPR fame called, Going Nucular[sic]. I'm still at the beginning but it's proving very enlightening. Nunberg, a linguist who specializes (according to Wikipedia) in lexical semantics, writes about the various ways our word-choice has transformed over the years- shaped by our environment and culture. I bought his book on a lark, literally picking up the first paperback with an interesting title because I had to break a hundred.

At the very beginning, he hits upon something anyone with an interest in synthetics has considered, however obliquely. He talks about how the word "plastic" shifted from something that indicated status and modernity to a word that has fallen out of vogue, a word that indicates superficiality, the cheap, the disposable, and waste. However, chances are, most everything in your modern life has some quantity of plastic in it. Even something like a spiral bound notebook, a very basic invention, might have a thin layer of plastic on the cardbard cover. Pens, which used to merit the actual business of "pen repair" are now throwaway plastic tubes. Even in more expensive pens that use refill cartridges, those cartridges will have some quantity of plastic.

Of course, not all plastic is created equal. In the AMC hit show, Breaking Bad, where the main character is a chemist who is forced by his cancer and financial situation to make and sell crystal meth, this is illustrated when they want to dispose of a body by dissolving it in acid. This scene will be with me for the rest of my life simply because it was so satisfying for me to watch. He specifically requests his partner (a non-chemist) get a large plastic tub with a resin identification code that labeled it as LDPE. These are the little "recyclable" icons with a number inside that you see on plastic products.

Plastics are made up of long chains of molecules called polymers. This gives plastic its characteristic flexibility. In the case of LDPE, the plastic is fairly non-reactive with concentrated acids. (Though if you throw an organic solvent on it, it will practically "thaw" before your eyes). His partner, repulsed by the thought of having to cut the body up to fit into the two containers, decides to use the bathtub. The bathtub is made of conventional ceramic (basically clay that has taken on a structure similar to glass) and is attacked by the strong hydroflouric acid solution and we get a (literal) bloody mess when the partially decomposed body pours through the floor into the hallway below. Hydrofluoric acid, I might add, is extremely dangerous. Most simple, strong acids will merely burn you. HF is absorbed through the skin very easily and acts as a poison since the fluorine binds strongly to the calcium ions in the bloodstream. These ions are critical to the function of our nervous system and muscles. It's essentially a rudimentary neurotoxin (though some neuroscientists may prefer to use the term more restrictively).

It's the characteristic nonreactive nature of plastic that makes it so useful, and so harmful to the environment. While recent studies have shown that plastic can in the right conditions, degrade naturally, the vast majority of plastic waste will continue to pose an environmental hazard indefinitely. Plastic breaks down mechanically over time, mixing with soil and entering the food chain. This is how plastic got to be such a dirty word. Plastic was the material of the future for a while. Disney had an exhibition called "House of the Future" where the entire structure was made of plastic. Legend has it that the wrecking ball essentially bounced off of it when the time came to tear it down. With increasing environmental consciousness (and presumably, hippies) the plastic craze died down.

Despite the fact that plastic can be recycled (the resin codes I mentioned earlier were designed to facilitate recycling) it's an energy intensive process- one that inevitably leads to more emissions. This is why the mantra of the environmentally conscious is, "Reduce. Reuse. Period." Some attempts are being made at creating plastics that do chemically degrade. The only problem with this is that one of the things that makes plastic so useful is the fact that it doesn't break down easily over time. Still this may prove useful for such things as single-serving beverage bottles, disposable cups, straws, etc.

Alas, modern life is simply not possible without plastic. Remember the computer and your car's dash. Laptops are affordable and portable because they are made of plastic. They're also more resilient and tolerant of drops and shocks than they would be otherwise. Similarly, in an accident, if your airbags fail, you don't want to slam your face into a wood, steel, or aluminum surface. Also, imagine the money you save on gas driving a car not entirely made of metal and wood.

I'm not saying that it is entirely impossible or futile to eliminate synthetic plastics from our world, but it does no good to be in denial of the challenges that face scientifically-sound environmentalism. There needs to be acknowledgment on some level that plastic isn't going anywhere. We should be reducing and reusing as much as possible until a more permanent solution is found. A metal canister/cans for drinks, paper cups, and less packaging are all steps that can be taken to reduce the amount of plastic that ends up in the ecosystem. Energy-efficient systems and infrastructure for plastic recycling and disposal are going to have to be critical areas of development in the future.

The Nature in Humanity

2010-01-28T14:57:00.006-05:00

There's something to be said about how we humans make a point of endlessly categorizing and labeling things. It's certainly useful, since part of what has made our continued survival possible is our ability to recognize patterns and forecast phenomena. It's also what has allowed us to create such highly sophisticated systems like governments, markets, and technical infrastructure. It also gets us in trouble. The same instinct that tells us that two sticks rubbed together get hot enough to make fire also tells us that we should eat only chicken before a big baseball game. A more common (so common we rarely consider it) failure of our pattern seeking ways manifests itself in our fidelity to the artificial categories we create. All dichotomies lose their significance at some level of consciousness. Whether or not someone is an American is irrelevant when a doctor is suturing a deep cut. On the other hand, it would be extremely relevant to a German soldier in the Second World War. Context determines significance. People arguing over how to categorize things are frequently trying to reconcile semantics. Sometimes though, a dichotomy is so functionally useless that we effectively call it false. The one that separates technology from nature is particularly interesting to me today.

I was reading an interesting post on the Bad Astronomy blog regarding the potential end to the Ares 5 program. As I was reading down the comments, I came across one in particular that struck me as problematic in a number of ways. The commenter, David, let loose a diatribe about "technological civilization" and essentially argued that we had ruined the planet and are all doomed to irrevocable extinction. (Believe it or not, this actually fits into the context of the discussion going on there.) I pointed out to him that overpopulation and the concept of population collapse aren't simple things to predict and model. I assumed he had watched the conspiracy and paranoia-laden "documentary" called Zeitgeist. I've been running into more and more people who have apparently seen it and swear by its precepts. I haven't seen it, but from what I understand, overpopulation is an important theme. I said that Malthusian model of population growth, that of exponential growth, was too simple to describe the real world phenomenon of how population fluctuates. I specifically singled out the formula P(t)=Ce^(kt) as being insufficient, where C= the initial population (or quantity- depending on what's being measured); e=Euler's number; t= time elapsed; and k=some constant growth or decay rate. (Different people use different variables, but the basic equation is the same.)

This formula for exponential growth and decay isn't useless, it does adequately describe true exponential growth, and you can use it to describe the decay of radioactive materials quite nicely. The problem is that the human population doesn't work that way for a number of reasons. As an extreme case, see the Chinese population, where the male-to-female ratio is being artificially increased. The Malthusian mathematical model doesn't work as well when male-female parity can no longer be taken for granted (though across short periods of time, it can be predictive across within one order of magnitude). Other factors, such as contraception, disease, fertility, sexual selection, and mating frequency all complicate matters quite nicely.

All of this is sort of tangential to what this post is about, namely why nature and technology are really part of the same edifice for all practical purposes. The response by David to my response was, "As it turns out, I happen to spend my time in Nature and have observed that everything which has a beginning also has an end. " (Notice the capitalized "N" in "Nature".)

Later, responding to someone else, he says,

"I am not at all impressed by human technology and I pity anyone who is so easily impressed. I wouldn’t destroy a living planet for the sake of technology, to do so makes as little sense as destroying your kidneys so that you might rely upon the technology of dialysis.
Technological civilization is a dead end.

Technological civlization is already dying right in front of our eyes.

Shall we continue to destroy the Earth for the sake of machines and drive humankind extinct in the process?"

Then, "Well, now that you mention it, that is precisely the case. A species which has destroyed its only home doesn’t merit any special favors from God or Nature."

It's obvious from his tone and the context we get from culture that he views technology and scientific advancement as being somehow at odds with nature. Yet if we look at history, the term "naturalist" was essentially synonymous with "scientist". One of the most prestigious scientific journals, one which publishes peer-reviewed articles in the physical and biological sciences, is actually called, Nature. The name isn't designed to deceive, quite the opposite. Scientists, and by extension, technologists, are all observers and users of nature. How we define the bounty of nature, however, is simply more expansive than I suspect David would define it.

Living off of nature, is to a scientist, unavoidable. Nature provides us with energy in the form of the fundamental forces of electromagnetism, gravity, the weak nuclear, and the strong nuclear forces. Scientists and technologists don't ask favors from nature- quite the opposite, we are bound to obedience. It is only by understanding the laws and restrictions nature places on us that we can improve our lot.

The tradition of observing nature is more than simply looking at the ecology, flora, and fauna of this world with our eyes. Richard Feynman, a physicist, wrote in his memoirs about ants he watched as a child, and shuttling them from place to place. He would observe how they formed paths and navigated. Yet the difference between this, and the use of a mathematical formula, such as the one I wrote above, to make determinations about the world around us is also the observation of nature. If mathematical logic is not an immutable feature of nature- imagine the chaos. Suddenly one ant joining another on one day is two ants, but tomorrow they could be negative three!

Instead what David seems to do is define Nature as the exclusion of humanity. Yet, this makes no sense. humanity must interact with nature. Everything that makes humanity what it is, from its biology to its behavior and consequent machinations; is defined, restricted, and ruled by nature.

This proposal in certain civilizations at certain periods in history would be deemed heretical. This way of thinking, at least superficially, is nigh paganistic. After all, isn't it God (or some other entity or set of entities) that defines, sets into motion, or rules our existence? While I wouldn't argue that scientists identify as Neo-Pagans it is clear that scientists, at least on some level, acknowledge the autonomy of nature as a phenomenon.

The dichotomy that David wishes to express is not internally consistent. Technology and mankind are as much a part of nature as anything else. That said, he is right that extinction is inevitable. Yet the reasoning and the way he chooses to derive this knowledge (by deliberately choosing to exclude those principles of nature that fit into his artificially narrow dichotomy) have lead him to believe our extinction is nigh, and not just unavoidable.

The reason I bring this up at all is because it's such a common and conventional way of viewing "nature". Nature is the world around us, plus us. A world where we do not exist, is by definition impossible and unnatural- the same way a world where light does not exist or interact is only a hypothetical, an imaginary reality and fun game we can play in our heads. It does no practical good and makes no sense to abstract humans out of the category that is nature, even if nature is synonymous with ecology. Instead we must continue to understand our role in nature and how we manage to obey its laws.

Pardon the Dust

2010-01-27T13:53:00.004-05:00

Alrighty, after some procrastination, I've moved all comments and commenting over to a new system powered by DISQUS. I've also gone back- waaaaay back in the archives and struck out at spam comments with my mighty delete button. So all those offers for drugs and Miley Cyrus sex tapes (I know- WTF?) are now officially cleared from my blog. Most of this spam was, for whatever reason, in Japanese.

There are some added features and functionality. My personal favorite is the flagging feature. After enough people flag a post, it will magically disappear. For now, I'm just hoping it'll help with spam. I've disabled avatars because I think they're just an annoying waste of space unless a majority of people are using them. Tags should work. Posts older than sixty days are closed to commenting. I didn't want to do that, because while digging around and deleting spam that was deliberately placed in older posts I found people were still leaving relevant comments. I may find a way around this, but for now it's something I'll live with.

Anonymous commenters should still be able to comment. Let me know if that's not possible.

Also, to all the nice people who left comments imploring that I write more: Aww shucks, thanks!

Let me know if something goes wonky.

My blog commenting policy remains largely the same as ever, and much of it is unnecessary since I don't run a particularly popular or controversial blog, but it's nice to have:

1.) Don't be a dick. (Ripped from Wil Wheaton's blog.)

2.) It's my blog, and I can delete any comment I choose. Comments that allude to a non-existent constitutional right to squirt digital diarrhea all over a discussion will be deleted with the almighty fury of a cocaine-addled baboon that just got laid off and has discovered that he will need retraining to work a similar job at lower pay.

3.) There are no swear-word restrictions on this blog. I may not swear as artfully as for example, Kyle Finchsigmate over at The [now defunct] Chem-blog, but that doesn't mean I have a problem with it. Just try to be imaginative is all I ask.

4.) Speaking of language, I will assume any comments made primarily in languages I do not understand are spam. These will be deleted unless you provide me with some indication in a language I do understand (or at least understand enough) that you are human. These languages are: English, Arabic, French and Spanish.

5.) Refrain from posting or linking to defamatory or illegal content. Note to international visitors: I live in the US, so as far as I'm concerned, illegal and libelous content is what's defined here in the US as illegal and libelous. If you want to say, "God, the nation, Barcelona" or "Homeopathy is bogus." and it's a risk you're willing to take, knock yourself out. However...

6.) Try to stay on topic. If you want to talk about the merits of Emile Durkheim's ideas on structural-functionalism and how it relates to episode #3 in the second season of Lost- then I had better have said something about it on the post. (Also, if you actually do try to discuss Lost in particular, I will try to find a way to digitally hurl massive objects at you.)

7.) Not technically a commenting policy, but I don't check the email as religiously as you'd probably like. This goes doubly so for people who want me to sell shit for them. I'm not averse to putting a up an ad or two, but seriously- can you at least try to relate your product to chemistry or science? Failing that, can you at least sell something interesting or remotely useful to my readers?

In Case You Forgot

2009-08-19T18:06:00.003-04:00

... just how unabashedly batshit some people used to be in this country:

Who Needs Perspective When Fear Sells?

2009-08-19T04:40:00.002-04:00

I keep telling myself that this is a chemistry blog and I should write about chemistry more. I think it would be kind of fun, for example, to do a nice little primer/tutorial on pH or pushing electrons. Unfortunately every time I sit down and scan the web, I come across some very seriously misinformed views and anti-science paranoia. I find I’m like a moth to a flame, I can’t resist the impulse to rebut all the burning stupid out there. Lately it’s the Daily Mail, a UK Tabloid, that’s getting under my skin. They have another scare story about vaccines, this time focusing on the swine flu vaccine.

I thought I’d write a post about it, but at the time I was just too fucking bored with this sort of bullshit. I did however email the story to a bunch of people who make it their business to care about this sort of thing and Phil Plait, the Bad Astronomer, emailed back with Steve Novella’s take on the ridiculousness of the Daily Mail’s insinuations.

All of Novella’s points, as he himself highlights, are essentially expressed in the article. What the article does however, and it’s painfully obvious they’re doing it, is play down these points and play up perspective from a vocal minority of people with dubious authority and tenuous relevance to the situation at hand. So much of it is framing, and I can’t help but find it extremely distressing. If framing is a substitute for facts, then we’re in real trouble people.

Summer Movie Time

2009-08-19T02:56:00.002-04:00

I'm a huge fan of the movies. This year there have been some good and bad ones. This summer's collection included a fairly predictable Transformers sequel. It was loud and mindless and worse than the first one. That said if you're into watching transforming robots battle each other, none of that really matters and you'll probably think it's pretty decent. I know I did. Sometimes, we all need to watch a Michael bay film to melt the wax in our ears. I do understand if that doesn't really carry mass-appeal (though the amount of merchandise out there begs to differ). Lately I did catch two good movies I can recommend to just about anyone, though.

The first was one I caught with a few friends, we were planning on seeing GI Joe initially, because one person in the group really wanted to see it. It soon became clear that no one else did however, and we quickly shifted to District-9 [Trailer]. Judging from the reviews of the former, our decision was wise. I really enjoyed District-9. The movie is set in Johannesburg, South Africa. The movie itself is in English (and alien with English subtitles.) When I was in high school, I met a lot of Afrikaners working as expats in the UAE. I never did learn much Afrikaans from them, though I did pick up on some of the more choice swear words. (I also learned some of the lyrics to a cheesy country song, but that's a story for another day).

The movie is framed in part as a documentary, but this gives way periodically to pure plot sequences. The plot of D-9 has some obvious parallels to the days of Apartheid in South Africa. However I also saw some parallels to the large-scale mandatory detention centers in Australia. The aliens' origins are something of a mystery. They arrive in a tremendous floating craft that hovers over Johannesburg. The only clue we're given as to why the aliens (called "Prawns" because of their appearance) can't seem to express any strategic or intellectual sophistication comes from a brief glimpse of an entomologist, theorizing that the creatures are merely workers that have been separated from a hive mind. They live in shanty-towns in horrible conditions where humans maintain some semblance of order by questionable means. Our protagonist is a naive bureaucrat who suddenly finds himself in the middle of his company's program to replicate Prawn weaponry (which humans can't use since the technology is bio-active). Some people think the allegory is too obvious to be compelling, but I disagree. I think people are simply choosing the most convenient allegory- the apartheid one which is certainly there, but there's a little more going on here.

I especially like the weapons and the way the aliens and humans interact. The aliens and their weapons and craft aren't invincible beyond the realm of plausibility. They're advanced, sure, but a human missile can still do a number on them. It always bothers me a little when humans use a missile on an alien technology and it sits there impervious. Are the aliens working off a different periodic table? Here humans can melt metal no matter what galaxy it's from. It's a little refreshing. There's also a surprising amount of gore and general disgustingness (blood, amputation, necrotic tissue, dissections, crushings, etc.) I'm not too bothered by that sort of thing, but sensitive people might want to take that into consideration. I highly recommend the movie, especially if the alternative is Yet-Another-Hasbro-Toy-Turned-Feature-Film.

The other movie I recommend may not be for everyone because it's a children's film. It is another Hayao Miyazaki/Studio Ghibli film. I've been a big fan of these for a while now. They're well made and imaginative stories about (usually) plucky youngsters thrown into fantastic situations. Ponyo [Trailer] is no exception. It's the story of a goldfish that befriends a human and with magic goes through a metamorphoses to become human. It's very far-fetched but a lot of fun if you want someplace to take a younger relative. What surprised me, (and I'm really not trying to inject science into this for no good reason) was the amount of scientific commentary slipped into the cartoon. There are references to the Cambrian Explosion, the Devonian, and the names of a few ancient fish are mentioned. There was an element of the movie that irritated me personally, but probably won't affect most people. I've mentioned before that I'm trying to learn Japanese and despite knowing better, I had actually forgotten that this movie is originally Japanese but dubbed into English. I found myself seeing words on the screen that I could pronounce but not understand, or characters that looked vaguely familiar but which I couldn't place. When I got home I tried looking up a few of them, but it's difficult to "look up" a character in Japanese if you don't already know how the word is pronounced. I still don't know any other way of doing it except by stroke count alone- which is guesswork. It's a bit of a wake up call as to exactly how little I know.

Those are the two movies I can recommend, but there were two previews that caught my interest. (You can pretty much guess which preview went with which movie.) The first is The Princess and the Frog. Really the appeal for me is all about the unabashed high quality 2D animation that Disney was moving away from until now. I like 3-D movies and all, but 2-D has a unique aesthetic appeal that can't be matched. I still think that Disney's best cartoons with the exception of Toy Story were all traditionally animated masterpieces. Then something happened (I don't know whether it was Eisner or what) and Disney became all about churning out tacky forgettable nonsense that you couldn't pay me to see even if I was a child. I think this will have its own charm:

The other is Zombieland, the word "zombie" is in the title, and really that's all I need to know. The trailer however, is also extremely promising:

DIY Seismometer

2009-08-15T19:41:00.001-04:00

I’ve been doing some research on the internet about earthquakes in Japan, as part of my ongoing all-inclusive research on the country before my visit. In doing so I came across some instructions for building your own seismometer. You can use it to detect tremors from all over the world, as well as underground nuclear tests. I just thought this was exactly the really cool, sciency type of thing I just have to share.

When Pigs Fly

2009-08-13T18:33:00.003-04:00

There is a serious element to a lot of the idle talk about swine flu. The severity of the disease was overestimated, and press reports exaggerated. However, given the available information and our understanding of influenza strains, health authorities responded rationally and within reason all over the world. (With some notable exceptions.) That said, the flu could mutate, and even cases of seasonal flu can prove fatal to vulnerable populations. The initial panic and misinformation about the disease may have lead to a world that is a little more complacent and a little more skeptical of infectious threats, however credible. This has opened the door to an insidious cynical views of swine flu and government health authorities worldwide. This past week a few stories called to my attention some of the more outlandish and dangerous claims about the disease.

Our affliction is international, and we begin in Kuala Lampur with a certain “Dr.” V.M. Palaniappan and his claims. He’s a doctor of ecology, so I’m calling him Mr. in the context of medical advice, which is what journalists should do when quoting someone outside their field of proven expertise. The link above goes to his blog, which I don’t recommend visiting unless you have an appetite for the crazy. According to the article,

“Avoiding masturbation and homosexual activities are among preventive measures one could take against Influenza A (H1N1), according to an eminent practitioner of complimentary therapy.

Dr. V. M. Palaniappan said that such activities caused the body to develop friction heat which in turn, produced acid and made the body hyperacidised.
"Thus, the body becomes an easy target for H1N1 infection," he told Bernama, emphasising however, that normal sexual union between members of the opposite sex was absolutely safe.”

I make no claims to an expert understanding of human immunity, however the claims here are preposterous when subjected to any logic. “Friction heat” produces acid? That alone is a highly suspect claim. If he had argued that physical exertion lead to lactic acid buildup in the muscles, it would at least make sense. However he is arguing that heat leads to increased acidity of the body (which I can only read as bloodstream). I can tell you right now that unless you’re boiling water off of a system, raising the temperature is unlikely to affect the pH significantly. Argonne National Laboratories has some good information on pH and heat in general terms. This is not to say that temperature can’t effect pH and systems in equilibrium, but such changes tend to be very small, and humans have regulatory systems in place to stabilize both blood pH and body temperature.

When Mr. Palaniappan claims that “normal sexual union between members of the opposite sex” is not harmful, I’m lead to assume that he’s arguing that there is no “friction heat” produced in straight sex. Reading this, you have to speculate a little on whether Palaniappan can speak from any experience in this field. But wait! There’s more crazy!

“Dr Palaniappan recommends coconut water, which is alkaline, and therefore could be used as a herbal medicine for the prevention of H1N1.
For example, he said, those who felt feverish and developed a burning sensation while attending to a call of nature because of extreme acidity, could neutralise it by drinking coconut water, twice a day, for three days.”

Really? What if I drink it three times a day, for two days? Will I OD? Also, coconut juice is acidic, you ignorant jackass, most fruit juices are. It’s not alkaline* unless it happens to be opposite day over there in Southeast Asia. I don’t know about Palaniappan, but I have a digestive system, so eating or drinking usually means food and drink don’t get dumped directly into my bloodstream. They spend a little time in this organ (maybe you’ve heard of it) called the “stomach”. I’m not a “doctor”, but I’m pretty sure that that’s pretty much how it works. The stomach is full of this glorious reagent common to industrial settings and labs all over the world: Hydrochloric acid. At a pH of about 2, I wouldn’t say that’s terribly dilute either. Maybe he would know this if he paid attention in medical school. Oh wait, that’s right, he never attended medical school.

A short hop and a skip away, from the Indian subcontinent we have this video, which I would have embedded if it didn't obnoxiously start up as soon as you load the blog into your browser (you’re welcome). I’m already suffering from crackpot overdose after analyzing Mr. Palaniappan’s claims, so I’m going to have to be briefer with this clown. According to our yogi (who apparently has some really cool merch!) people with strong immune systems cannot get swine flu. Isn’t it cute when ignorant morons use modern scientific terminology without actually being cognizant of what they’re talking about. The immune system can’t protect you from viral threats your body hasn’t already been exposed to, and no amount good health will help you if manage to get enough viral particles into your system. Actually, people with strong immune system are more susceptible to the effects of swine flu. The reporter also added that the Yogi advised people to wear face masks in crowded spaces. Putting aside for the moment problems with face masks (though I wouldn’t discount their utility completely) the Yogi obviously doesn’t understand germ theory, so what does he think face masks are going to do? I’m just trying to understand his thinking here.

Finally we arrive home (well, home for me anyway) here in the good ole US of A. What is it this time? Crystal healing? Alternative therapies “they” don’t want you to know about? Nope, it’s our old friends, the nitwits over at the National Vaccine [mis]Information Center. The anti-vaxers are at it again. I’ll bet these are the same people who take their dogs to the beach and don’t clean up after them, ruining it for the rest of us. Really their philosophy thus far has been, “Herd immunity doesn’t exist, and we’re going to do whatever the fuck we want.” But, I’m griping, let’s get to the video of Barbara Loe Fisher:

There’s a lot here to discuss, and this is made harder by the fact that she doesn’t really say anything. Mostly it’s a lot of scary noise about a swine flu vaccine. Note she emphasizes that the vaccines are experimental. She’s very fond of the word, but if you go to the NVIC website, it’s clear that they’re also against vaccines that aren’t experimental. I don’t like giving these people link love when unnecessary, so you’ll have to find it yourself. WebMD (a site with real doctors!) has some accurate information about why testing is being fast tracked and given to children first. It’s not being “tested” on children as Fisher so blatantly mischaracterized it. It’s the lifeboat principle, in this case, pregnant women and children first. Also, and this is important, this flu vaccine is not significantly different in design from seasonal flu vaccines. The technology has been tested numerous times in general principle, though I don’t expect anyone from the NVIC to understand anything about that.

She also quotes a number of disorders and statistics about children with various conditions, and leaves it hanging in the air. These figures are meaningless if she can’t say anything about a causal relationship between them and vaccines, or between them and alleged “vaccine damage.” The whole video is about scaring people, not informing them. She talks about “well informed choices” and while I’m all in favor of giving people the full rundown of information, the simple fact of the matter is that at the end of the day, medical professionals know better. Otherwise we wouldn’t have doctors at all.

Well, it’s been quite the roundup of the ignorant, the clueless, and the dangerously stupid. Of all of the bullshit peddlers, I think the people from the NVIC spout the most dangerous line of nonsense. At least the other two maniacs didn’t exactly discount modern medicine completely. NVIC is actively promoting that we put children at risk, with their line of crap and I’m not particularly tickled about it. If there is in fact a cure for swine flu, the vaccine will be our best bet, and if these ignorance damaged half-wits have there way, it’s a cure that will be rendered useless by their unjustified paranoia. This is where ignorance hurts us all.

*Updated to add: I forgot to mention that “alkaline” is not usually a term applied to this sort of thing to mean “basic”. Alkalis are technically only soluble bases with OH- groups. It’s interchangeable in common English, but there is in fact a distinction. I really need to do a post on acid-base chemistry.

Movie Marketing Goes Horribly Awry

2009-08-11T21:29:00.001-04:00

So by now I’m sure you’ve seen the trailers and ads for Roland Emmerich’s latest disaster [of a] movie. 2012 is supposedly about the end of the Long Count in the Mayan calendar and, because of some hocus pocus bullshit you can look up on Wikipedia yourself, means the world will end that year. Under normal circumstances I’m okay with this. Not only do I have no problem with bad movies being released into theaters, I even watch them (I don’t give a shit about the critics, I liked Transformers. Part two natsamuch.) Where does the marketing team go too far?

Well I was listening to Are We Alone on my mp3 player while grabbing a nice greasy hamburger and they were discussing disaster movies [Direct mp3 here]. Apparently some people have taken the marketing for 2012 seriously. When Seth Shostak interviews astrobiologist David Morrison from NASA, Morrison reveals that he has received numerous panic-stricken emails from people, especially teens about this 2012 end of the world scenario. It gets serious when one teen writes him suggesting that suicide is a better alternative to sticking around for the end of the world. Apparently there is a website, where if you don’t read the fine print (and what naive teen does?) it looks like a legitimate program to try and save humanity. In fact, it seems to combine the design elements of Obama and NASA’s websites. This is what Morrison had to say on it,

“…I don’t mind disaster films and I don’t mind science fiction films. What I object to here is they are marketing it as if it’s real. And they’ve even created a completely fake website for the Institute for Human Continuity that is telling people that this is a real danger and that they can join a lottery to be saved in an underground shelter and so forth. They treat it… They scare people, by making it seem like a real event.”

I say if the marketing is going to convince people this is real, then they shouldn’t worry so much about the profits and proceeds from the film, since hey, the world’s coming to an end soon anyway, right?

I’m tempted to lay this at the feet of the people who have fallen for the premise of the movie, but there is whole credulous world of websites all over the internet unconnected to the movie ready to reinforce newfound belief in this nonsense. I prefer to pity the dupes and punish the dupers. There’s nothing really to be done about this except tell people that it’s nonsense as you find them. Nonetheless it’s frustrating to see people fall victim to such an absurd myth.

Ah well, why don’t you have fun with this 70s style trailer of the movie:

Captcha is now turned off.

2009-08-11T01:46:00.002-04:00

Comment moderation for posts older than ten days will remain turned on for a while. But as long as the bots stay away from the blog for a while, I'll leave word verification off.

Someone is an Idiot

2009-08-11T01:34:00.001-04:00

…and that someone is (drum-roll please!) Adrian Michaels of the Telegraph.co.uk! The Telegraph, at least the online edition since I can’t read the print edition from across the pond, I think reflects poorly on British newspapers, and this sort of article is precisely why. Adrian Michaels seems to think Muslims* are zerging** the EU. Putting aside for the moment the various cryptic and xenophobic statements and lets look at some of the “facts”, shall we?

According to Adrian Michaels (these are direct quotations):

“Only 3.2 per cent of Spain's population was foreign-born in 1998. In 2007 it was 13.4 per cent.”
“Europe's Muslim population has more than doubled in the past 30 years and will have doubled again by 2015.”
“In Brussels, the top seven baby boys' names recently were Mohamed, Adam, Rayan, Ayoub, Mehdi, Amine and Hamza.”
“Another forecast holds that Muslims could outnumber non-Muslims in France and perhaps in all of western Europe by mid-century.”
“Austria was 90 per cent Catholic in the 20th century but Islam could be the majority religion among Austrians aged under 15 by 2050…”

Oh so shocking! Except it isn’t really true. I know, journalists are too busy to fact check these days, so I had to get off my lazy ass and do some snooping (You know, the kind I don’t have to go much further than Wikipedia for). The numbers below correspond to the claims above:

The vast majority of Spain’s immigrants are from other EU countries. (The top source of immigrants being Romania increasing at a whopping 1,187% over seven years.) Morocco is second (at 141% increase over seven years), but you have to go pretty far down the list to get to another Muslim-majority country. While the statistic regarding Spain’s foreign born population may or may not be right, I fail to see how it supports the argument for a dramatic invasion of Muslims considering the proportions of immigrants.
I’m having a great deal of difficulty verifying the claim that the Muslim population of Europe (find me the population of Muslims in Europe in 1979- harder than you’d think, huh?) has doubled in the past thirty years, but the claim that this can be dependably extrapolated into a doubling of Muslims in the next fifteen years is moronic. Moreover, those claims I can source seem to come from conservative think-tanks. (More on that in a second)
While these Muslim names do in fact top the list of popular baby names in Brussels- here is an article that makes the point that native Belgians are choosing less traditional and more unique names for their children, making it hard to attain the critical mass necessary to make the top of the list for any given “Belgian” name. I find it interesting that baby names are cited while actual population statistics are not.
France doesn’t collect statistics by religion, making the same kind of extrapolation in (2) suspect since any census of a Muslim population or birthrate there is done by people interested in such information for various reasons. What little information there is does not inquire as to religious beliefs or practices and the term “Muslim” in France remains imprecise and reflects a certain attribution to ethnicity.
Sure it could be. Pigs could fly as well, given wings and adequate propulsion systems.

This article brought to mind something I was reading from the BBC the other day (evidence that the BBC is a much better source of information) which discussed the imprecise nature of demographic predictions and basically featured European statisticians imploring people to calm the fuck down. This is why claims that the Muslim population in Europe will double in fifteen years is so ludicrous. Populations are fluid, and tend to cap for various reasons. My father is one of eight kids, I’m one of four. Chances are I won’t have more than two (not because I’m extrapolating, but because I’m sane.) Unhindered exponential growth is for bacteria, and I’m sure Michaels would like that comparison with Muslims. As would the readers who swallow this offal whole.

It’s scare tactics for a European population that has become increasingly less tolerant of diversity. I get harassed at US airports enough, but the frequency has been decreasing considerably over the years. I don’t find myself in the melanin room at immigration as often as I used to. Meanwhile I’ve found that airports in Europe are truly hostile to someone with a name and birthplace such as mine, even with American citizenship. So much so that I have no desire to visit Europe for any reason. When stopping in Europe I prefer flights where I do not have to leave the plane. There is absolutely nothing I want to do in Europe.

I am convinced that conflict between Muslims and non-Muslims in Europe will rise and part of it will be due to the short-sighted stupidity of Europeans who decided that speech laws were ever a good idea, both the sense of entitlement and oppression immigrants will feel because of such laws, the ghettoization and subsequent concentration of Muslim communities stemming from distrust, and finally the wage disparity and class disparity that have immigrants at the bottom rung. By contrast, most Muslims in the US are not nearly as insulated, speech and religious practices of all kinds have been liberally tolerated, and upward mobility remains relatively more attainable for legal immigrants to this country. I only hope that this xenophobic nonsense doesn’t get spread out here, not that some people aren’t trying.

*Ones who aren’t even seekrit, like Obama!

**YES. I am using the word way too much for one week. I haven’t used that word in a while and I’m suddenly quite taken with it.

The Great Zerging of August

2009-08-10T21:35:00.006-04:00

PZ Myers has written a take down of the Creation “Museum” on his blog. For those unfamiliar with the so-called Creo-Zerg, Myers with the Secular Student Alliance and a number of other interested folk got together and did a tour of the museum. For those unfamiliar with the term “zerging”: It’s from a strategy employed in the old strategy video-game Starcraft. Zerg was one of the alien races you could play as and they could generate multiple units faster than the other two races in the game and overwhelm them long before they could even develop defenses. The idea here was less to overwhelm, and more to ridicule. It was supposed to be a bunch if people asking tough questions, and by all accounts it was a smashing success.

I was very religious and devoted in my teens, being raised that way. I have relatives who buy into creationism, though I myself believed completely in evolution while managing to be very religious at the same time after a very brief struggle to adjust. Part of what helped was the knee-jerk reactions of people who I tried to discuss the matter with. Their knowledge of evolutionary theory seemed so short on facts I quickly became convinced that they merely accepted it to be false without any real consideration. So, to separate myself from the pack I looked deeper into the matter and emerged with a clear grasp of the idea. This spirit of contrarianism has served me well.

So it goes with the myths and misconceptions evangelized in the “museum”. It is simple denial and omission of the evidence. In that respect it is exceedingly mundane, and not worthy of comment from someone who was never there. I did have a look at one of the pictures that incensed me (click to embiggen):

Picture is from the Pharyngula post linked above.

The “Tower of Babel” nonsense really gets to me because of its description of the origin of what we identify as “racial differences” (which are no more than superficial differences given cultural significance). Also, see Update #2 at the bottom of this post for more fail. The idea that our individual phenotypes emerged from random dispersal is ridiculous. If I take any population of blonds and disperse them in various countries, their hair color will not change significantly over a only a few generations so long as they continue to couple within the gene pool. the same goes for any population of dark-skinned people, or people with epicanthal folds of the eyelid. The only way these things change are as a result of adaptation to the environment over a long period of time. Not merely “a couple of generations,” as the poster suggests (these people believe in a 6,000 year old earth). It changes because of natural selection for people with these traits in a population. In fact, in genetics, polydactyly (having extra digits, in particular, a sixth finger) may be an autosomal dominant trait*. What this means is that like unattached earlobes, having a parent with the trait dramatically increases your chances of having unattached earlobes. Yet there aren’t that many people running around with a sixth finger, simply because it likely proved to be maladaptive and decreased survival odds for people with the trait.

It’s offensive to reduce phenotypic diversity to some vague unproven differentiation process that has inclined some people to believe that “smarter” folk from Babel chose certain areas, while “dumber” races from other inhabited still other areas.

This brings me to the other offensive aspect of the poster/”exhibit” which argues for a universal pattern for all modern languages. BULL. SHIT. Ancient Sumerian was not the first language for one thing. Unless you believe hunter gatherers communicated by grunts and cave art was drawn by the Devil to mislead you. Sumerian is unlike a great many languages, and belongs to its own linguistic family. In preparation for my Japan visit I’ve been learning Japanese and can tell you that similarities between Japanese and English, the Romance languages, Slavic languages, and Arabic are few and seemingly coincidental. Japanese is so utterly different from all of these that to argue that it is based on a similar format is nonsense. (Unless by format and grammar, you mean the language has words, and is spoken.) There is something called universal grammar, but to argue that this is based on Sumerian more than it is a function of neurological limitations and function is ludicrous. There’s a lot we don’t know about language and this attitude that Sumerian holds all the cards and all the answers is arrogant and retards impulse to explore further and objectively.

In fact it seems so much of the “museum” is about the exact opposite of exploration, as PZ Myers makes clear. These are people who are content with the answers they have and are made very uncomfortable to go beyond them and explore their basic assumptions. It is anathema to science, and yet they demand equal representation of their views in the scientific community. Science frequently features challenges to old ideas, yet challenge theirs and it’s considered persecution. You can only answer such nonsense with rational analysis for a brief period, and then much like the “birthers” the next step is simply ridicule. This is why we cannot and should not tolerate people who try to inject intelligent design (which is watered down creationism of the same absurd sort) into school curricula. Forget about the separation of church and state for a moment, this garbage is utterly without merit. If for that reason and no other, it deserves to be buried as an unfortunate chapter in human intellectual history.

Update: PZ Myers is linking to other accounts of the visit through his blog, here.

Update #2: The Babel exhibit also has a Hebrew fail:

Update #3: Greg Laden is um- laden, with more links.

We Want These People To Stay in Business?

2009-08-10T17:39:00.000-04:00

I never have and never will understand the compulsion some people have to keep the health insurance companies in business. The dynamics of private insurance (see "Adverse Selection") are such that insurance benefit-holders are already paying for the ill-health of others. A public single-payer model will do little to change this. Meanwhile, private insurers continue to engage in exceedingly immoral methods of evading their responsibility to their clients, as is dramatically illustrated in this case.

I'm unimpressed with the arguments made in favor of the status quo. Perhaps it's because I never really bought into the libertarian tripe about how we are all rational actors working with the best information available to us. I also never bought into the right-wing conservative myth of benevolent industry.

Disgusting

2009-08-05T17:48:00.003-04:00

A group of "animal rights activists" has burned down the vacation home of Novartis CEO Daniel Vasella and took his mother's ashes after vandalizing the gravestone. Their objection was apparently Novartis's contracting to a lab in the UK called HLS. As the article points out, Novartis hasn't even been doing business with them for a while. Not that this excuses the behavior either way.

I've been trying to fathom the thinking of these people, and I'm sorry, I just can't. I even looked over PETA's materials on animal testing (don't waste your time) just to see what could possibly in any sort of twisted perverted way make someone think this sort of thing is okay. It's more evidence that these people are dangerously out-of-touch.

Objection to Context

2009-08-04T21:54:00.001-04:00

Every scientist has biases and ways of thinking that may enter into their work. The good scientists presumably are conscious of this and try to keep their biases out of the science, and only espouse those ways of thinking that allow them to make progress. Of course, scientists are human beings, and whether it was Einstein’s faith in certainty (an objective reality, if you will) or Newton’s dabbling in alchemy, even the greatest scientists have had their lapses. Generally, I would like to imagine a certain amount of respect for diversity of background and motivations in the scientific community- so long as such diversity does not noticeably impact the work done to discover nature’s laws. This is why I’m a little distressed to see a few instances of people objecting to the appointment of Francis Collins to head the NIH- because he’s Christian.

Certainly his detractors wouldn’t put it in such terms, but that’s really what it is. I need to get more specific here, and say that I’m motivated to write this by PZ Myers’s recent post on the matter, so I’ll be addressing his arguments in general. I have no special love of Christianity- even as part of a residual sympathy, since I was never raised Christian. Perhaps I have other sympathies that come into play here, but I’ll save it for later. I don’t have a special dislike of PZ Myers, whose blog I read regularly, though I find it somewhat hit and miss. In case you were wondering, I think this was a miss. The most relevant portion of his post as far as I’m concerned is this:

So what's different about Collins? He doesn't keep it to himself. He is openly and avidly evangelical, brags about adding religious messages to NHGRI announcements, and recently built a high-profile website that promotes evangelical Christianity. I don't mind a Christian in charge of the NIH, but I do object to a missionary, especially one who has said some awfully stupid things about science, being put in control of such a large chunk of our country's science budget.

Certainly, he’s an evangelist for the religion, which seems to be Myers’s main objection to his appointment. However evangelism is part of the religion for some people, and if he wishes to use spurious arguments in support of that evangelism, that is entirely his business so long as government money isn’t spent in this pursuit. To argue that the objection is not to his religion, but to his evangelism is bullshit. Evangelism is part of the package, and you can’t argue what can or cannot be a part of someone else’s religion. This is especially true considering that the arguments Collins uses are part of his own rationalization of his beliefs rather than active dishonesty on his part. If it interferes, then it interferes, and he shouldn’t have the job. If his statements are merely stupid or wrong, but don’t affect his job then we should be consistent and complain about Joe Biden constantly.

He also does not have major issues with current scientific consensus on evolution. He may well be a theistic evolutionist, but in practical terms, this means very little in terms of how he will run the NIH as an administrator. He has demonstrated his ability to tackle scientific problems.

Fundamentally, Collins hasn’t really done anything beyond think a certain way and have certain beliefs which he has evangelized as part of his personal life. Are these beliefs incompatible with science? Yes, in some respects more than others, but once again he has not demonstrated a willingness to allow them to affect his duties at the NIH. While he may use such terms as “God bless,” or similar language in his new position, it remains within the bounds of acceptable political speech considering that President Obama himself uses such language. Much as I dislike it, it’s not a disqualifying factor.

We can’t spurn every scientist with a religious bent from positions of importance simply because they are evangelists who have made spurious statements. We are all evangelists who have made spurious statements whether they involve superstition or not. We will persist in being such people all our lives because it’s part of the nature of believing in anything, whether or not it involves pie in the sky when you die. There can’t be a minimum standard on spurious statements and evangelism of questionable beliefs when unconnected to a lack of scientific contribution, and which allows us to prejudge the person’s abilities and remove the benefit of doubt. If there is such a standard, I won’t sign up for it. I wouldn’t want to be part of the scientific community. I’d rather be a crank and a crackpot working in isolation than a prejudicial pompous ass. This sort of attitude is what Richard Feynman found so objectionable about the National Academy of Sciences in his lifetime (I have no idea whether this has changed since). He perceived it as an association preoccupied with keeping people out as a means of considering the “in-group” special (my words, not his).

I wouldn’t have gone into science if I was not at some point, religious. That’s my bias in this. We are all motivated to do science by different things, and in many cases, religion is a part of a scientist’s initial push to explore. Usually it’s grounded in a sense of wonder about God’s creation. Sometimes it fades as a motivation, as it did in my case, whereupon the person finds another reason to continue doing science. Other times it only gets stronger. I learned a long time ago that resenting people’s motivations to do the same things you do is a waste of time and energy. Why should I care that someone contributes to charity because they think God commands it, when someone else gives to charity to assuage personal guilt over some event in their lives? Ranking and rating is for the military, consumer reports, and video games. It doesn’t change the nature of their contribution, nor in the grand scheme of things when I’m dead and buried and humanity no longer exists, make me a “better person” than they because my motivation was empathy.

It is what it is, a flash of objection based on nothing more than a man’s religion. If it can be demonstrated that his integrity as a scientist is affected so severely by his religious beliefs that he is not qualified execute his duties, I wouldn’t be writing this. His religious beliefs, however much he chooses to evangelize, are not a disqualifying factor in and of themselves. Instead, what I see is people making accusations of a vague possibility that his beliefs may affect his performance with no more than innuendo to back these assertions. It’s petty and does nothing but run a fissure through the community with no apparent benefit to the advancement of science or knowledge.

Science Theater? Where?

2009-08-03T20:50:00.001-04:00

I’ve always thought there were was something cinematic about science. In my own head, I tend to float concepts across visually. Still not much science appears on the big screen. Drama is a function of human interaction, and science can only be an accessory here. Still, the history of science is replete with stories worth telling, whether it’s the story of the first atomic bomb or the murder of Nikolai Vavilov.

I was taking a walk yesterday, and listening to This American Life on the radio. It was a rerun, but I listened anyway, and when the show was over I was about to change over to another station or an mp3 when the next show came on. It was an LA Theater Works: The Play’s the Thing production. Called Breaking the Code, it’s a play focused on the life of Alan Turing, and mostly focused on his personal interactions and his homosexuality. Some of his work was discussed, including a remarkably clear and concise description of the Enigma machine. All in all, it was a good play, and I prolonged my walk to listen to it. In the interludes and at the end, it was announced that this was produced as part of a 17 play series sponsored by the Alfred P. Sloan Foundation back in 2008. All of them are stories of science. Others from the series apparently include the story of John Robert Oppenheimer and a story about a researcher who starts doubting her faith in her own racial superiority. I have been trying to find all of the items in the series somewhere, but so far I’ve been unsuccessful. The LATW website is a pain to navigate and NPR’s page on the matter 410’d or 404’d or something.

I’m always in favor of a good story or anecdote, scientific or not. I’m not a big fan of mixing art and science just for the sake of mixing them, but then, I’m also not a big fan of people acting like they’re oil and water. It seems really interesting and I w0uld like to find more, and it’s a real pity that it’s not easily Googled. The best I could find was here, and I haven’t had a chance to listen to these, but if anyone knows anything about where to track these things down, throw me a bone will ya’?

It Happens That Often?

2009-08-03T19:37:00.001-04:00

I guess it must, if someone has to set up a charitable project, right? Meet Andrew Jacono, he does reconstructive surgery on victims of domestic violence. The part that got to me?

Seventy-five percent of injuries from a domestic partner are made to the head, face, and neck. The men are trying to control a woman’s ability to leave the relationship. They want them to appear ugly and disfigured.

Audience Participation FTW!

2009-07-28T15:06:00.003-04:00

Too cool, I had to repost it after I saw it on Cosmic Variance.

World Science Festival 2009: Bobby McFerrin Demonstrates the Power of the Pentatonic Scale from World Science Festival on Vimeo.

What Do You Give An 800 lb. Gorilla?

2009-07-27T23:05:00.004-04:00

Whatever s/he wants. Now.

Such is the case with AT&T's blocking of 4chan. For those unfamiliar with the imageboard, I advise you to stay that way if you have even a shred of innocence left in you that you want to preserve. I would not want to mess with 4chan, hell- when the ever outspoken PZ Myers wrote about it, he said,

"I am not a great fan of 4chan (actually, I tremble in fear at even mentioning them, so I have to respect them—I'd rather piss off the Catholic Church than 4chan), but in this case I have to be on their side without reservation."

To be honest, I'm a little apprehensive mentioning them as well.

There's plenty of analysis on PZ's post and what he links to. Instead I'll just say that the 4chan community is very, VERY, proactive, and behind their power is their anonymity and ability to coordinate quickly and devastatingly. On the one hand, you don't want to make it sound like they can launch a nuke if they felt like it. On the other hand, there's a small part of you that thinks,
"Maybe they could..."

Nihon!

2009-07-24T21:29:00.002-04:00

A few days ago, I resolved to do at least one thing in the next year that I've always wanted to do, but could never get around to. So I'm going to Japan! Specifically around May-ish to July-ish. I'm still trying to decide what season I want to encounter. Preferably when tourists hit an all time low is ideal for me.

I intend to go for a month to have fun, to eat the food, see the sights, take in the culture, and really make an adventure of it in general. I've already started learning a little Japanese, though I understand that many Japanese people usually speak some English. In general I think I'd be more comfortable if I could carry a conversation with a stranger. Actually, if I have my way, I'll be proficient in the language before I leave. There are people who say that it's one of the harder languages to learn, but I've learned a long time ago that simply considering something "hard" often becomes the singular significant barrier to completing any task. I really do mean any task. For now I'm going to resist the urge to go off on a tangent about this.

If you can't figure out the title of the post, to the Japanese, the name of their country is Nihon or Nippon, depending on what they're reffering to. My understanding of usage is that Nihon is the country, and Nippon is the State. I'm not going there to see the state, whatever its merits or demerits.

It wasn't a random spin of the globe, I've been interested in Japan in particular for a while. My father was a practitioner of Judo when he was younger. Like so many parents who enroll their kids in an activity, I got enrolled in a Judo class at a very young age. It was a lot of fun and I remember enjoying it immensely. Ever since then I've been interested in Japan, though my interests go beyond martial arts.

As far as I'm concerned, it's going to be a total lark. I really have no business there and no one I know there. Aside from some lodging arrangments I'll basically be parachuting in, a prospect I find especially appealing though I'm not sure why. When else will I get a chance to do something like this? During a grad program? As a post-doc? Fuhgettaboutit. I'll go now. Er- May. You know what I mean.

The Next Time You See A Pregnant Woman...

2009-07-23T20:40:00.002-04:00

...tell her she's glowing. Not just because it's a mere cliche, but because it happens to be literally true. We are all glowing, emitting radiation, even if it isn't visible. Or isn't it?

New research has come out that shows humans glow in the visible spectrum. It's a very small amount of light, and you can't see it with your weak pathetic human eyes. Scientists have used special cameras to pick it up.

Via Built on Facts.

Breaking the Mold

2009-07-17T20:39:00.001-04:00

I don’t have cable, but I recently got to watch the two latest episodes of AMC’s hit show, Breaking Bad by watching them online. First of all, I think AMC should look into Hulu, which is where I’m doing most of my TV watching these days. For me, it’s about scheduling more than anything. I’m sorry, but TV has never been a priority. I’m willing to watch your shows and the ads that come with them, but only during those times I feel like it. Anyway I digress.

I loved the first season, and couldn’t wait for more. Watching the second season, it looks like I can expect to get a similar kick out of the new episodes. There’s a strong element of suspense, and while normally the “fish-out-of-water” theme is cliché, the characters here are convincingly out of their depth in ways that make sense and take it beyond a mere gimmick. It really does an outstanding job of storytelling.

I get a special kick out of watching it. Partly it’s the familiarity of the language and ideas, and the fantastic aspect of it. Take for example the use of hydrofluoric acid to dispose of a body. I would absolutely want nothing to do with the large amounts of HF used in real life, but it was an interesting thing to sort of fantasize about. Not that I fantasize about disposing of bodies in acid (much). It also sort of got me interested in the history of meth-manufacture to an extent that worries my friends a little. I won’t start making it of course, because I live in an apartment and I don’t want to lose my security deposit. Or get arrested. What I was surprised to hear was that the Hell’s Angels did their methamphetamine production as a near total synthesis.

What this means is that they didn’t go out and buy Sudafed, which is very close to the structure for methamphetamine (including the “newer” Sudafed), but they actually went through the process of making it using more basic chemical components. I don’t know whether they were actually knowledgeable of theory, but it’s interesting to think about motorcycle gang chemists.

It’s great to have a protagonist that’s a nerd, and someone who is actually passionate about science t’boot. While selling drugs isn’t exactly noble, we understand the motivations. All too often the scientist is part of the group of evildoers, the mastermind of some dastardly plot. Then Superman swoops in and punches his kidneys out. Even in other fiction where science isn’t involved, the nerds aren’t really there to save the day. Take the Harry Potter novels as an example. Harry Potter isn’t the best wizard in the group, or the most knowledgeable. Really Hermione should be doing all the ass-kicking, all Harry has going for him is luck of the deus ex machina variety and a sidekick who’s mostly comic relief. Fortunately, Breaking Bad rises above that tradition.

Sure, there are elements of the story that need work. Especially the son, who is really underdeveloped as a character, and doesn’t seem to serve much purpose. What Breaking Bad really has going for it though, besides a kick-ass premise, excellent acting, and a mastery of suspense, is that we’re given a main character that we actually give a damn about. At it’s core it’s really the time honored story of the working stiff who has to take drastic measures to save his family.

Uub Gets Its Birth Certificate

2009-07-14T22:49:00.001-04:00

Old news, but nonetheless worth commenting on, element 112, known by it’s “placeholder” name Ununubium will soon have a proper name. The team at GSI who synthesized the element proposed the name Copernicium with the symbol Cp. the name is pending approval, but the chances are it will be accepted without much fuss. Traditionally, IUPAC gives discoverers a lot of leeway in naming and name like Copernicium is unlikely to raise serious objections.

When Glenn Seaborg and Edwin McMillan produced plutonium in a lab in December of 1940 they were given the opportunity to name the new element and propose its symbol, the one or two Latin letters that would serve as shorthand for the element worldwide by scientists speaking all languages. The name of the element was named after what is now no longer the ninth planet of our solar system, and Glenn Seaborg proposed Pu as a tame joke. It was a play on the exclamation “Pee-yew!”. He did not expect IUPAC to approve the symbol, but it passed without any so much as a murmur.

People who have looked a periodic table in the last decade may look with puzzlement at the various elements near the bottom of the periodic table without formal names. The reason for this is that there is some debate over which research team discovered the elements first and whether the elements were actually discovered in the first place. The elements are made in miniscule amounts, are highly unstable and decay very quickly. Part of the difficulty in synthesizing the new element is getting evidence of its existence. This can be done by detecting decay products in statistically significant quantities. (If any nuclear chemists out there are reading this and think I’ve gotten anything wrong, please correct me.) The level of relative uncertainty over discovery has lead to at least one case in particular of alleged fraud.

IUPAC seems to have finally decided that in the case of element 112 that the scientists at GSI have priority it its discovery. I think it’s great to have be alive for the naming of a new elements. The size of atomic nuclei is severely limited by the physics governing the particles in the nucleus, and there will come a day when we will no longer be able to create new elements. Some people argue that we’re there already.

Stop the Presses!

2009-07-08T19:12:00.001-04:00

Google is going to compete with Microsoft.

Oh... it's on now. It's on like Donkey Kong!

The Link-ness Monster

2009-07-07T22:50:00.001-04:00

I’ve seen any number of things on the ‘tubes today that makes me want to share:

The 114th Skeptic’s Circle. (Bonus: Stuff on Alchemy!)

Azmanam’s Chemical Dictionary is now available from the ScienceBase servers. I strongly commend him on his effort and fully expect it to become a gold standard by the time he’s done tinkering with it. For non-chemists out there, ever write something using specialized language in your office suite and have a red squiggly line under every other word? Well that’s what happens way too often if you use words like “azonide”, “solvation”, “dimethylmercury”, or “1,3,7-trimethyl- 1H-purine- 2,6(3H,7H)-dione” I highly recommend adding it to your browser’s spell-checking repertoire as well.

The European Space Agency is going to make its own manned space vehicle! This is a Good Thing(TM) because with the space shuttle being retired, the only people going into space will have to rely on the Cosmodrome at Baikonor. Not that I’m paranoid about the Russians hogging space, but if we can’t be a two planet species, can’t we at least be a two launch pad one?

Speaking of the Russians… good news: We’re working together to slash our nuclear arsenals. Bad news: People are still clinging to antiquated notions about the utility of missile shields.

Finally, since I showed you how to make iodine in the last post, now you need something to do with it. Well, if you’re still waiting on the book. You might want to try this (taking all appropriate precautions of course):

Quick and Easy Home Iodine Tutorial

2009-07-07T13:21:00.001-04:00

I’ve been wondering a long time when the DEA will stop chasing its tail and stop all the pointless restrictions that make life harder for the home chemistry experimenter. This video just goes to show that the worst thing the DEA can think to do in terms of legislation, is to mildly inconvenience no one. Someone over there needs to get their head out of their ass and realize that not every civilian out there with a test tube and half a brain is cooking up some meth. Restricting reagents isn’t even half the battle, and if it is, then you’ve already lost.

Any half-way clever sophomore organic chemistry student could probably think of a dozen mechanisms (of admittedly varying efficacy, hazard, and yield) to make the stuff using reagents that wouldn’t raise anyone’s eyebrows even purchased in industrial quantities. I’m not an advocate for getting people hooked on crystal meth, but I get so pissed off at pointless DEA restrictions I get strongly tempted to publish a complete guide to circumventing all of them. Anyway, the video is a nice little tutorial on making iodine, and I have the book, an excellent resource for students starting out in experimental chemistry:

WANT. BADLY.

2009-07-06T23:01:00.001-04:00

I’ve never fancied myself a book collector, though I do have a handful of rare/out-of-print/autographed/limited-edition books of very limited monetary value. Believe it or not, they’re all either things given to me, or impulse buys. This, however, is the one book I can honestly say I really want to own.

It’s particularly funny because my interest in flammables and energetic materials is fairly constrained to not accidently making them go boom in the lab and enjoying fireworks/Mythbusters. Still, something about the book intrigues me, perhaps it’s the fact that a book like this can actually go out of print! Unbe-fucking-lievable.

Trying To Have It Both Ways (Hint: You Can’t)

2009-07-06T22:45:00.001-04:00

Listen to this politician talk with a straight face about uranium mining and a 6,000 year old earth in the same breath:

General[ly Useless] Hospital

2009-07-03T17:03:00.002-04:00

I Was Right! (Again!)

2009-06-17T14:45:00.003-04:00

I remember once writing a post when I so sick I couldn't even spell "quackery" right and could barely get my point off the ground. I mentioned how Zicam was probably not going to help you with your cold as a homeopathic treatment. There were a few comments from some people arguing that it's really the zinc in the formulation that was helpful and tried to sort of defend Zicam. Well, it looks like Zicam does work- just not at fixing colds. Apparently the zinc in the formulation can rob you of your sense of smell! So my mistrust of non-FDA approved treatments pays off yet again! Now if you will excuse me, I'll be over there in the corner, patting myself on the back.

Edgar Allen wha-?

2009-06-03T15:19:00.001-04:00

If you got to this blog from a comment on Bad Astronomy. Yeah- that was totally me, and totally Poe.

Stuff On The 'Tubes

2009-06-01T14:17:00.004-04:00

A few things to call to your attention:

1. Silence is the Enemy: At The Intersection, Sheril Kirshenbaum blogs about the plight of women in Africa where where in some parts, 75% of women are raped, and the alarming trend continues to grow. Visit the page, give it a once over and see what you might be willing to do to help.

2. The shooting death of Dr. George Tiller is all over the news. Bitch PhD has a good link post on the subject.

3. World Refugee day is coming up (June 20) and I intend to blog about it. The UNHCR site has yet to set up a dedicated page though.

4. I have a post up at Chemistry-Blog about the way constants are given superficial treatment in science education.

5. Scientists over at Nanosonic have made electrically conducting, nigh indestructible rubber.

6. Newsweek, yes- Newsweek, tackles Oprah's quackery.

7. I leave you with a lolcat to brighten your day:

A Great Pro-vax Video

2009-05-29T16:37:00.001-04:00

Einstein Book Review

2009-05-20T19:30:00.003-04:00

Many of the biographies I've read suffer from the same major problems. They're long, boring, and don't do their subjects any justice. Fortunately the Walter Isaacson biography of Einstein was none of these things, though it does suffer from the two traditional weaknesses of biography: First, where it repeats itself often, unnecessarily eliminating the possibility of suspense. Second, putting its subject on a pedestal.

Of course Einstein was not in any sense a terrible person, or a politician or leader, so being in awe of him isn't such a bad thing. However, I think Isaacson would have done better to show how Einstein mellowed as he aged. We all know that Einstein's ideas and politics changed, but it's unrealistic to assume a person's personality remained static throughout his or her life. While Isaacson readily and repeatedly noted Einstein's distance from people he failed to highlight that Einstein's rough edges could sometimes be quite sharp when he was younger. Take for example Einstein's biting remarks to Fritz Haber. Einstein was extremely disdainful of Haber's attempts to be a "good German", a fact Isaacson acknowledges. However, some of Haber's letters to Einstein lamenting his own status as a second-class citizen received rather cold replies. One can of course argue that this was deserved, but I think there is some difference in Einstein's approach to confrontation when he was older compared to when he was younger. Still, while too many biographers are quick to de-emphasize faults, Isaacson avoids this for the most part.

There is one aspect of the biography that disturbed me initially, but by the time I had finished I realized that I was working off of bad information. Isaacson talks a lot about Einstein's God. Perhaps it is a reflection on me more than Isaacson but I felt he spent far more turn on this than necessary. Though as I stated earlier, I had learned something I did not know. Based on a widely publicized letter and one that Richard Dawkins in particular flaunted--I got the distinct impression Einstein was a strongly avowed Atheist. However Isaacson makes it quite clear that this is not the appropriate conclusion based on Einstein's own letters and statements. Eisntein's own words make it quite clear that he was Deistic rather than Atheistic. Throughout his life Einstein only denied the existence of a personal God- however strongly he denied it.

I have never really felt Einstein's opinions on this matter to be particularly important regardless. Whether you're an active atheist or deeply religious. Einstein was wrong about any number of things (being quite the human being). Richard Dawkins made one good point in the recording I linked to above, that Einstein's views shouldn't be accepted on the basis of authority- whatever his views may have been. Simply acknowledging that Einstein was a genius without really comprehending the nuances of his specific brand of genius, just to associate him with a personal cause, is quite appalling.

As for a verdict on the book: In general it's a good biography that seems to prize accuracy and relies heavily on quoatations of primary source material to make its points for it. It's a little long, the price paid for being thorough- but the lulls and lags are few and far between.

Science v. Media

2009-05-14T17:15:00.005-04:00

I had a recent comment on one of my older posts that reminded me why I'm writing a series of chemistry primers (at this stage, I may as well say I'm writing a pop-science book- there's so much to cover). The media really sucks at presenting and explaining science. It's a common gripe among professional scientists, amateur scientists, and educated followers of science. I didn't always feel this way, myself. I used to be quite optimistic about the state of science reporting.

There is an excellent book, covering much of the ground science has broken in understanding the natural world by a science journalist called, The Canon: A whirligig tour through the beautiful basics of science. It was written of course, by New York Times writer Natalie Angier, one of the better reviewers of scientific information. Mary Roach also, must be commended for her work in Stiff, Spook and especially Bonk, where she literally became a part of the scientific process. Miles O'Brien was always an excellent science reporter when he was at CNN, though his talents weren't appreciated there. He now writes at TrueSlant.

With science reporting of this caliber, I used to wonder just how bad things could be, what everyone was complaining about. It was then I realized that I'm a product of my own consumption- I don't watch the same TV the average American watches, and I don't read the same books. I mostly ignored the science sections of the papers because I got my information from places like ScienceDaily, science blogs that are linked to the right, and looking over journals themselves using my university library's privileges (they don't get ACS though- which bugs the crap out of me). Recognizing that, and looking around, I saw why scientists are so quick to complain, and I now complain with them.

When you watch television, say Larry King, a ridiculous story on UFOs suddenly becomes a two-sided controversy. Never mind that SETI has been working for years to answer the question, "Are we alone?" and that astronomers spend hours upon hours looking at the night sky. Larry King chooses to use the mantra of "equal time" to make his show more entertaining- not more accurate. Newspapers aren't much better- scary headlines sell papers and generate advertising revenue. The breast implant issue in the 80s was a clear case of a panic induced by the media. Reports of several published case studies involving women who blamed their connective tissue disease on their implants turned into a nation-wide scare. One woman who could not afford to have her implants removed picked up a razor blade and tried to do the job herself[1]. We know that such implants are not connected to connective tissue diseases. In fact, there was nothing more than a few anecdotes. Meanwhile every fringe scientist and quack was given a voice by the media.

The media is interested in entertainment and the sale of advertisement. Selling information is not in their job description because the consumer isn't paying for it. There is the popular delusion that a person is being informed by policies like "equal time". Maybe on matters of opinion this works- where everyone is working off the same set of facts, but there are many different approaches to the issue. For example, generally everyone in a community is entitled to have their ideas heard on what should be done with taxes, for example. In science however, being presented with an "equal time" discussion is like being given dog food and being told it's pâté. There is no way a layperson can determine just who is full of shit. (Some would argue there is no way to tell dog food from pâté, but I digress.)

The scientific method allows scientists to be wrong. Just because a study is published, it doesn't mean it's right! One study is exactly that- just one or a handful of scientists who think they have a good idea. Think of it as an internal memo to the scientific community, "Hey guys! I think we've found something here!" Then, other scientists who clearly understand the issues surrounding the experiment or study try to reproduce the results. This brings us to what at least one chemist terms ISHTAR. Irreproducible SHit That Aggravates Readers. When results cannot be reproduced, depending on the field, it can be extremely frustrating. Often enough, it means that the research was done improperly, or the scientist misinterpreted the data.

Generally, a study like this is a "no harm, no foul" kind of deal. If you publish too many such studies, your credibility may suffer and you'll have trouble getting funding, but there are no "science cops" who will come and hang you by your toenails while they tickle you mercilessly with a big purple feather. Scientists are wrong, happens all the time- then they go back to the drawing board and try to be right about something else. Or they can try to improve the data to see if they missed anything. Or they go completely the other way and conduct an experiment to definitively prove their old idea wrong. What a good scientist does not do is stomp their feet and run to the press claiming persecution. Like I said- there are no science cops to do the persecuting. The press of course, doesn't care, it snaps this sort of story right up. It isn't interesting to have a person on television talking knowledgeably of state-of-the-field research. What really gets a caterpillar in a viewer's shirt is when you pit the bumbling boring bozo against the magnetic malicious maverick. Controversy! Conflict! Sensation! Responsibility? Drama! Dynamism!

Not that this is new, Einstein's theory of relativity was sensationalized by the media, a case that is slightly different because Einstein was actually proven right. Yet in their rush to execute their rhetorical flourishes, the newsmen got things wrong, a writer in Berlin who interviewed Einstein wrote,

"It was from his loft library that he observed years ago a man dropping from a neighboring roof-luckily in a pile of soft rubbish-and escaping almost without injury. The man told Dr.Einstein that in falling he experienced no sensation commonly considered as the effect of gravity."[2]

One of the headlines on the article was, "Inspired as Newton Was, But by the Fall of a Man from a Roof Instead of the Fall of an Apple." Of course, this pleasant tale is entirely untrue. Einstein was fond of thought-experiments, and imagined the consequences of painters falling, riding along light beams, watching lighting hit rail tracks, and two dimensional insects. He couldn't have seen the sight described by the reporter because he wasn't living in Berlin to observe anything from that loft-window when he conceived on the theory! It was pure sensationalism.[3]

Sadly, even journalists who have a healthy respect for the scientific method and scientific discovery get things wrong. Roger Ebert famously once tried to write parody, only to have it fall flat. Not that journalists shouldn't try at all. His review of Star Trek mentioned a number of scientific issues that were right on the money, though it's mostly about the entertainment value- which is fine. Good reviews focusing specifically on the science can be found here and here.

Some have argued that things won't get better unless scientists make their fields more transparent. While I agree that more could be done to reach out to the public, this is only part of the solution. That's because the problem isn't the way scientists communicate to the public. The problem is the way the media serves as conflicted intermediary between any group and the public. The fact needs to be widely disseminated and cried loudly from every rooftop: "The media does not serve its consumers!" The media sells the attention of its consumers to the highest bidder, more attention, more money. The problem is greater than science in the media, the problem is the media, its methods, and the conflict of interest posed by its hunger for advertisers. This issue reaches well beyond accuracy in scientific reporting.

[1]Offit, Paul. Autism's False Prophets. Columbia University Press: New York, 2008. p.75.
[2] Quote is from- Isaacson, Walter. Einstein:His Life and Universe. Simon & Schuster: New York, 2007. p. 266.
[3]Ibid.

Resources for the Pro-Vax Crowd

2009-04-29T22:23:00.002-04:00

Todd W., a commenter on Bad Astronomy, has created a new site, Anti Antivax for people who want the raw figures about vaccination. It's great. I admit to being biased because I made inquiries into contributing.

It Doesn't Have To Be This Way

2009-04-26T15:10:00.005-04:00

"A lie can run round the world before the truth has got its boots on." -Terry Pratchett.

See this video:

Heart-wrenching, isn't it? I cannot begin to express how furious this makes me. There is a reason we invented the vaccine. It didn't start with Big Pharma or with any kind of conspiracy. It started with deadly diseases having their way with humanity. Mindless, deadly, and efficient organisms with agency and a biological impulse to survive and perpetuate through human hosts are the reason we vaccinate. Vaccines have a purpose the way hand-washing has a purpose. It's not some mere rite of passage every infant goes through. It's a necessary prophylactic against diseases that have killed in the past and know no sympathy for future hosts.

People talk about autism like it is the absolute worst disease to afflict humanity. It isn't. Not by a long shot. If vaccination levels drop below a certain threshold, people will die. Wishful thinking and fearful hope that diseases we no longer see will remain at bay is not enough. We don't apply such positive-thinking to infant seats in cars. Physics has no sense of sympathy, biology no morals. These diseases will come for the weakest members of the population first- not last. Parents struggling to make a decision about whether or not to vaccinate may hem and haw over the narrative presented by Age of Autism, or Jenny McCarthy. These are people who express a narrative, a compelling chain of events to explain why we vaccinate. I am here to tell you that this narrative is false. I am here to tell you that this movement of storytellers have an insidious background all their own.

The story behind vaccines is simple- with its own ups, downs, and immoralities. People were getting sick and in many cases, dying, of smallpox. A man named Edward Jenner noticed that a segment of the population was not dying, not getting sick- milkmaids. Instead they got a very similar disease, cowpox, and if they did become ill- tended survive. Only later would we would understand how and why this seemed to work, but at the time Edward Jenner simply made the inference that getting cowpox was enough to confer an immunity to smallpox. Then he did something horrible, he tested his idea on a small child- first infecting him deliberately with cowpox obtained from one of the lesions of another infected person. Then he gave the boy smallpox, obtained in a similar fashion. Smallpox was a death sentence. In 1967, it killed two million people. Depending on the type of smallpox, it can have a mortality rate as high as 75%. This boy survived and from the Latin vacca, meaning cow (as in cowpox), the vaccine was born.

As you can see, the patron saint of the vaccine is no saint at all, his experiment was something we would never do today. Yet as our knowledge of pathogens and disease grew, the more Edward Jenner's experiment made sense, the more we understood how to build on this, and create new and more effective vaccines. So we did. Do people make money selling vaccines? Absolutely. Is there an absurd amount to be had? Oh goodness yes. However, what is the significance of that? Is it really reason enough to cast aside volumes of scientific study on the subject? After all, do people make money selling food? Yes. Is there an absurd amount of money to be had? YES! Yet, we have yet to see someone campaign for an end to the consumption of food. Perhaps they don't have the energy.

I cannot teach people to fear the diseases that we no longer see (but will see, if and when vaccination rates drop). What I can do is tell you a story, the story of the people who would watch the world burn through their own dislike of water. In 1998 Andrew Wakefield, a gastroenterologist, published a study attempting to establish a link between vaccination and autism. Since then, 10 of the 13 coauthors have retracted their names from the study. Andrew Wakefield was not one of them. In fact, he was later found to have committed the cardinal sin of science: He faked his results. What has happened since then is a series of events that deserve a longer and more detailed evaluation than is fitting for this post, which is meant to be an introduction. However a few things stand out, such as Wakefield's attempts to capitalize on his "findings" by starting a clinical practice called Thoughtful House.

Celebrities such as Jenny McCarthy have glommed onto this movement, advocating non-vaccination, making claims for which they have no evidence. Meanwhile, the vast majority of the scientific and medical community understands and accepts the necessity and utility of vaccines. Who are these scientists and doctors? They are people like you and me, people who received educations in their specialty precisely because they sought truth in nature. They are people who vaccinate their children. They are often the very type of person who is working towards a cure for autism. So can vaccines really cause harm?

Kanatjan Alibekov was a biologist in the Soviet military infrastructure's bioweapons program. He later defected to the United States. In his work involving some of the most evil pathogens known to man, he was vaccinated many times, and in his book Biohazard he discusses the effect of those multiple, frequently untested, vaccines. The side effects are all auto-immune, and none of them are neurological. He talks about being allergic to eggs, milk, and other foods. He talks about having skin problems like eczema. He doesn't cite neurological difficulties. We know vaccines can have side effects, but we know what those side-effects are: they are listed on the box! Better than that, we understand fully how these side-effects come about, and can work towards eliminating them. Meanwhile, the people who claim autism is caused by vaccines can't offer even a guess at how vaccines might do so.

It is true Big Pharma is selling you a product, but it's a product that you just so happen to need. I don't ask you to trust them because I myself do not trust them, or even like them. They have done a lot of wrong in the past. Still, we know what they are selling, we can touch it, feel it, talk to the people who designed it. So too, we must lucidly and clearly understand what Andrew Wakefield and his ilk are selling. What they are selling you isn't a product, but a lifestyle. They are telling you, in the face of mountains of contrary evidence, that they and their small community are to be trusted on this matter and no one else. They are selling you an idea. It will cost you. It will cost you an exclusive faith in their small pool of abilities, and potentially the life of your child.

Don't buy it.

Should I Laugh or Throw Things?

2009-04-25T15:38:00.006-04:00

Via Pharyngula:

Sigh,

Study Buddies

2009-04-23T21:12:00.004-04:00

One of the things that strikes me as interesting about the way science is depicted in fiction is that it's rarely presented in terms of what is known, but rather it tends to be symbolized by its trappings. We know a person is a scientist not by what they say (unless it's "I'm a scientist."), but by their environment or what they wear.

A tour through a movie lab involves a whole lot of glass containers full of blue liquid which eventually turns a sympathetic character into a monster. Generally, there's not a lot of, "Oh my God! That idiot just drank my toxic copper sulfate solution! Copper Sulfate is a useful fungicide and is what they use to test your hemoglobin levels! Get a doctor, he's seizing!" Of course there wouldn't be anything like that in movies. Sure, sometimes you're in the mood for an informative science lecture about gamma rays. Really though, most of the time you just want to see Hulk smash (second one was decent).

Where this becomes an issue is when non-scientists get blinded by incomprehensible data. the average person wouldn't be able to toss a study out on its ass and call it cargo cult science just by flipping through it. In fact to a lawyer, a banker, a street vendor, or to *cough* a science journalist any kind of layman a crap study looks the same as a good one: Lots of graphs, equations, and sciencey type er... things. Yet sometimes, the graphs and diagrams are actually diversions. It's like someone got the idea, "Hey! let's throw lots of data in here and maybe no one will notice that we fail to prove our point!"

Take, as an example, just one of the many things wrong with the "ZOMG! 9/11 was an inside job!" study I mentioned a while back. They spend, if I recall correctly, ~25 pages talking about the properties of a sample ostensibly obtained from the day of the attacks. Yet, they don't go through a lot of trouble to ensure this is in fact dust from the Center. A lot of things got blown off by the wind that day, and they don't have any real way of knowing if the substance they claim to have found was from the buildings or blown off something else near the buildings. Then they do strange things, like treat a "control" paint chip in solvent and compare the effects. Yet, there are more than a few formulations for a paint, and more than few things it could be besides paint. Don't even get me started on the volatility of paint binders and the potential differences between old chips with evaporated solvent and new paint chips with residual solvent. I don't attack the experimental data proving the composition of the dust because I don't have to. The study lacks one of the most important things in science: rigor.

When a scientist say, discovers a new insect repellent. It's not enough to spray one piece of food with water and one with the repellent and put both on an anthill and then say it works. They might do this of course- if only to get a rough idea of what to expect and to help form a hypothesis, but they wouldn't get heavy into collecting data just yet.

In a simplified example involving one ant, they would take the two pieces and place them equidistant from the place the ant is going to be released (for the purposes of this example, I want you to imagine a tiny ant cage, mainly because I find the idea amusing). The two pieces of food are weighed to be equal and sprayed with the same amount of both the water (as a control) and the repellent. The ant is then released. This is then repeated hundreds of times until it becomes apparent that the ant is actually repelled. But wait! The light bulb in the test chamber makes one side brighter! There's a draft that may be pushing the scent one way and not the other! The ant is a lefty! A whole host of factors that have to be controlled for can easily render any experiment meaningless if you're not careful.

So how do we know when a scientific study is any good? Mostly, you don't- we have to rely on what scientists tell us- unfortunately. It is unfortunate that we can't always make truly informed decisions. This isn't much different from relying on a lawyer to tell you the law. There are a lot of things you can understand on your own. It may even be in your best interests or fun for you to learn those things. However, you wouldn't defend yourself if you were accused of murder. In a serious situation- you eventually resort to faith in an authority. Even if that authority isn't as competent as you would like. This is the unavoidable consequence of not being able to specialize in everything. The good new is that you don't have to trust just one person.

I once read a comment somewhere saying that cutting scientific funding only affects 0.000001% of the population. Being a complete geek, I knew he was full of shit. That would mean that in a population of ~300,000,000 Americans, there are 3 scientists. In truth scientist PhD's in the US come in at around 0.2%. By contrast construction workers come in at around 5%. They number in the hundreds of thousands, and that number only gets bigger when you take into account science is an international effort. It is a part of every scientist's job to hold others in the community to the standards of their field. So while a scientific consensus may eventually turn out to be wrong, by and large, trusting isolated cranks who don't interact (frequently by choice) with the community at large is not the wiser decision.

A Good Joke?

2009-04-21T14:37:00.002-04:00

Jokes are funny because of their relatability. The corners of my mouth twitched when this popped up on my feed reader (What's Hot in Google). Perhaps the people who are currently grad students will appreciate more.

Don't Worry- This Doesn't Happen in America

2009-04-16T13:48:00.002-04:00

Via BoingBoing:

The Shape of Things To Come

2009-04-14T17:19:00.006-04:00

I was working in the library the other day when I found this crawling up my jacket:

Hey little guy!

Fortunately I happened to have a half decent camera to take a picture of this inchworm, which is really a kind of caterpillar. I naturally went outside and released it into a bush to munch on some leaves. I admit it, I'm a buggist. If it had been a cockroach crawling up my jacket I probably would have gotten all eeky, smashy, stompy, killy; but I find inchworms, and especially the way they move, kind of endearing.

The scientific name of the family to which the inchworm belongs, and the moth it eventually turns into, is "Geometridae". It comes from Greek, meaning earth-measure. So does the word "geometry". It seems like a peculiar way to segue into a topic on chemistry, but chemistry is called the "central science" for a reason. This is a post on geometry, and how chemistry isn't just about the elements.

As you probably know, unless you live in a box or suffer from severe urbanitis, when caterpillars turn into moths or butterflies, they have to construct a cocoon. Cocoons have been used by humans for thousands of years, primarily to make silk and stay young. While I haven't heard of anyone making clothing from the silk of an inchworm, silks all serve the same function aside from being pretty: They protect the developing insect. Insect silk isn't as renowned for it's strength as that of their arthropod cousins, the arachnids; specifically spiders. However it's the same principles give both kinds of silk such high tensile strengths. The secret lies in their geometry.

When I had an argument recently with someone about vaccination, I mentioned that geometry is a major factor in how chemistry works. People who haven't gone beyond a sophomore organic chemistry class know what I'm talking about. It's often not enough for certain elements to be present in a compound to start guessing its properties, and this is especially true in biological systems. It's how these elements are arranged that can make all the difference. I cannot overemphasize how important this concept is. There are more than a few rules that organic chemists have generated over the years simply to describe geometries. They have arguments over structures, and expend considerable effort resolving the exact structure of a molecule. Over at the Curious Wavefunction there are posts on peer-reviewed research discussing the structure of hexacyclinol, if you want some idea of what that looks like.

In silks, spider and insect, the high tensile strength is primarily due to what are known as β- pleated sheets of proteins linked together. Proteins are huge molecules. We call them macro-molecules, containing potentially thousands of atoms. Beta-pleated sheets, as the name implies are arranged like the pleat of a skirt. This arrangment offers crystalline strength. The protein "threads" that link the sheets together are also responsible for strength. The precise way that these geometries interact to make silk so strong is something still not completely understood. A lot of work goes into the process of first discovering the precise arrangements of atoms in the large molecules that comprise silk, and then discovering how this arrangement translates into strength.

The proteins that make up these silks are on the elemental level: nitrogen, oxygen, hydrogen, and carbon (basically). Yet those very things could also be in a racing fuel. To start giving credit to these elements for the strength of silk based on their elemental forms would be ludicrous. It has a lot more to do with the how of elements bonding than the what.

Sometimes what may sound like minor variations in a chemical's structure actually amount to quite a lot. The best example of this is enantiomers. Look at the picture below:

Ladies and gentlemen, meet ibuprofen, perhaps better known to you as Advil or Motrin. It is your best friend when you have a headache. Or is it? Actually that is a picture of (R)-ibuprofen, the right handed form of the molecule. What you want is actually this guy:

They are literally mirror images of each other. However, only one really cures your headache fast. The (S)-ibuprofen (left-handed form) is the one that acts quickly to cure your headache. The right-handed form kind of screws around in your body a bit before actually turning into the left-handed form. You may not see how they are mirror images, but it becomes clear when you construct a model of them and hold them side by side. These molecules are chiral, the word "chiral" coming from the Greek word for "hand". Your hands are chiral objects. When you hold your hands in front of you, they are mirror images of each other, but if you set one hand on top of the other, the thumbs are at opposite ends. They are in effect, non-superimposable mirror images of each other. We call these enantiomers of each other. They have the exact same boiling point and melting point, but in your body, which is a chiral environment, they have different effects. Chirality is a big deal in biology. In fact, there is some evidence that the right-handed form of ibuprofen may actually slow down the action of the left-handed form. Enantiomers can be expensive and difficult to separate, though. This is why the ibuprofen you buy at the store is actually a mixture of these two forms. For now.

This post started with an inchworm and worked it's way into something much longer than I intended at first. It's just a sneak peek into the world of chemistry, it's my way of showing that it's more complicated than throwing two things together and getting a reaction. It's become my best attempt to date at expressing some of the complexity inherent in chemistry in layman's terms. I think it's important people understand that chemistry goes beyond the periodic table, and has depths that they may not be familiar with. I only hope it's been written clearly enough.

The Sound of Decay

2009-04-11T17:57:00.005-04:00

MAKE:Blog recently showed off an interesting sound installation that played strings according to the decay of radioactive materials.

The Doctor Will Sue You Now

2009-04-11T15:31:00.006-04:00

Ben Goldacre, of Bad Science fame, released this chapter of that same book into Creative Commons that could not make it into the first edition of his book for legal reasons. [EDITED TO ADD: I should say something for the American readers, when Goldacre talks about "nutritionists" he's using UK terminology- where "nutritionist" is not a regulated profession (in the UK, the regulated professional is called a "dietician"). These UK "nutritionists" make all sorts of outlandish claims not supported by scientific evidence. Qualified American nutritionists who do no more than advise people on healthy eating habits and study the effects that foods have on people are not what he is referring to. ] With his blessing, I repost the chapter here:

This is an extract from
BAD SCIENCE by Ben Goldacre
Published by Harper Perennial 2009.

You are free to copy it, paste it, bake it, reprint it, read it aloud, as long as you don’t change it – including this bit – so that people know that they can find more ideas for free at www.badscience.net

The Doctor Will Sue You Now

This chapter did not appear in the original edition of this book, because for fifteen months leading up to September 2008 the vitamin-pill entrepreneur Matthias Rath was suing me personally, and the Guardian, for libel. This strategy brought only mixed success. For all that nutritionists may fantasise in public that any critic is somehow a pawn of big pharma, in private they would do well to remember that, like many my age who work in the public sector, I don’t own a flat. The Guardian generously paid for the lawyers, and in September 2008 Rath dropped his case, which had cost in excess of £500,000 to defend. Rath has paid £220,000 already, and the rest will hopefully follow. Nobody will ever repay me for the endless meetings, the time off work, or the days spent poring over tables filled with endlessly cross-referenced court documents.

On this last point there is, however, one small consolation, and I will spell it out as a cautionary tale: I now know more about Matthias Rath than almost any other person alive. My notes, references and witness statements, boxed up in the room where I am sitting right now, make a pile as tall as the man himself, and what I will write here is only a tiny fraction of the fuller story that is waiting to be told about him. This chapter, I should also mention, is available free online for anyone who wishes to see it.

Matthias Rath takes us rudely outside the contained, almost academic distance of this book. For the most part we’ve been interested in the intellectual and cultural consequences of bad science, the made-up facts in national newspapers, dubious academic practices in universities, some foolish pill-peddling, and so on. But what happens if we take these sleights of hand, these pill-marketing techniques, and transplant them out of our decadent Western context into a situation where things really matter?

In an ideal world this would be only a thought experiment. AIDS is the opposite of anecdote. Twenty-five million people have died from it already, three million in the last year alone, and 500,000 of those deaths were children. In South Africa it kills 300,000 people every year: that’s eight hundred people every day, or one every two minutes. This one country has 6.3 million people who are HIV positive, including 30 per cent of all pregnant women. There are 1.2 million AIDS orphans under the age of seventeen. Most chillingly of all, this disaster has appeared suddenly, and while we were watching: in 1990, just 1 per cent of adults in South Africa were HIV positive. Ten years
later, the figure had risen to 25 per cent.

It’s hard to mount an emotional response to raw numbers, but on one thing I think we would agree. If you were to walk into a situation with that much death, misery and disease, you would be very careful to make sure that you knew what you were talking about. For the reasons you are about to read, I suspect that Matthias Rath missed the mark.

This man, we should be clear, is our responsibility. Born and raised in Germany, Rath was the head of Cardiovascular Research at the Linus Pauling Institute in Palo Alto in California, and even then he had a tendency towards grand gestures, publishing a paper in the Journal of Orthomolecular Medicine in 1992 titled “A Unified Theory of Human Cardiovascular Disease Leading the Way to the Abolition of this Disease as a Cause for Human Mortality”. The unified theory was high-dose vitamins.

He first developed a power base from sales in Europe, selling his pills with tactics that will be very familiar to you from the rest of this book, albeit slightly more aggressive. In the UK, his adverts claimed that “90 per cent of patients receiving chemotherapy for cancer die within months of starting treatment”, and suggested that three million lives could be saved if cancer patients stopped being treated by conventional medicine. The pharmaceutical industry was deliberately letting people die for financial gain, he explained. Cancer treatments were “poisonous compounds” with “not even one effective treatment”.

The decision to embark on treatment for cancer can be the most difficult that an individual or a family will ever take, representing a close balance between well-documented benefits and equally well-documented side-effects. Adverts like these might play especially strongly on your conscience if your mother has just lost all her hair to chemotherapy, for example, in the hope of staying alive just long enough to see your son speak.

There was some limited regulatory response in Europe, but it was generally as weak as that faced by the other characters in this book. The Advertising Standards Authority criticised one of his adverts in the UK, but that is essentially all they are able to do. Rath was ordered by a Berlin court to stop claiming that his vitamins could cure cancer, or face a €250,000 fine.

But sales were strong, and Matthias Rath still has many supporters in Europe, as you will shortly see. He walked into South Africa with all the acclaim, self-confidence and wealth he had amassed as a successful vitamin-pill entrepreneur in Europe and America, and began to take out full-page adverts in newspapers.

˜The answer to the AIDS epidemic is here,” he proclaimed. Anti-retroviral drugs were poisonous, and a conspiracy to kill patients and make money. “Stop AIDS Genocide by the Drugs Cartel said one headline. “Why should South Africans continue to be poisoned with AZT? There is a natural answer to AIDS.” The answer came in the form of vitamin pills. “Multivitamin treatment is more effective than any toxic AIDS drug. Multivitamins cut the risk of developing AIDS in half.”

Rath’s company ran clinics reflecting these ideas, and in 2005 he decided to run a trial of his vitamins in a township near Cape Town called Khayelitsha, giving his own formulation, VitaCell, to people with advanced AIDS. In 2008 this trial was declared illegal by the Cape High Court of South Africa. Although Rath says that none of his participants had been on anti-retroviral drugs, some relatives have given statements saying that they were, and were actively told to stop using them.

Tragically,Matthias Rath had taken these ideas to exactly the right place. Thabo Mbeki, the President of South Africa at the time, was well known as an “AIDS dissident”, and to international horror, while people died at the rate of one every two minutes in his country, he gave credence and support to the claims of a small band of campaigners who variously claim that AIDS does not exist, that it is not caused by HIV, that anti-retroviral medication does more harm than good, and so on.

At various times during the peak of the AIDS epidemic in South Africa their government argued that HIV is not the cause of AIDS, and that anti-retroviral drugs are not useful for patients. They refused to roll out proper treatment programmes, they refused to accept free donations of drugs, and they refused to accept grant money from the Global Fund to buy drugs. One study estimates that if the South African national government had used anti-retroviral drugs for prevention and treatment at the same rate as the Western Cape province (which defied national policy on the issue), around 171,000 new HIV infections and 343,000 deaths could have been prevented between 1999 and 2007. Another study estimates that between 2000 and 2005 there were 330,000 unnecessary deaths, 2.2 million person years lost, and 35,000 babies unnecessarily born with HIV because of the failure to implement a cheap and simple mother-to-child-transmission prevention program. Between one and three doses of an ARV drug can reduce transmission dramatically. The cost is negligible. It was not available.

Interestingly, Matthias Rath’s colleague and employee, a South African barrister named Anthony Brink, takes the credit for introducing Thabo Mbeki to many of these ideas. Brink stumbled on the “AIDS dissident” material in the mid-1990s, and after much surfing and reading, became convinced that it must be right. In 1999 he wrote an article about AZT in a Johannesburg newspaper titled “a medicine from hell”. This led to a public exchange with a leading virologist. Brink contacted Mbeki, sending him copies of the debate, and was welcomed as an expert.

This is a chilling testament to the danger of elevating cranks by engaging with them. In his initial letter of motivation for employment to Matthias Rath, Brink described himself as “South Africa’s leading AIDS dissident, best known for my whistle-blowing exposé of the toxicity and inefficacy of AIDS drugs, and for my political activism in this regard, which caused President Mbeki and Health Minister Dr Tshabalala-Msimang to repudiate the drugs in 1999″.

In 2000, the now infamous International AIDS Conference took place in Durban. Mbeki’s presidential advisory panel beforehand was packed with “AIDS dissidents”, including Peter Duesberg and David Rasnick. On the first day, Rasnick suggested that all HIV testing should be banned on principle, and that South Africa should stop screening supplies of blood for HIV. “If I had the power to outlaw the HIV antibody test,” he said, “I would do it across the board.” When African physicians gave testimony about the drastic change AIDS had caused in their clinics and hospitals, Rasnick said he had not seen “any evidence” of an AIDS catastrophe. The media were not allowed in, but one reporter from the Village Voice was present. Peter Duesberg, he said, “gave a presentation so removed from African medical reality that it left several local doctors shaking their heads”. It wasn’t AIDS that was killing babies and children, said the dissidents: it was the anti-retroviral medication.

President Mbeki sent a letter to world leaders comparing the struggle of the “AIDS dissidents” to the struggle against apartheid. The Washington Post described the reaction at the White House: “So stunned were some officials by the letter’s tone and timing during final preparations for July’s conference in Durban that at least two of them, according to diplomatic sources, felt obliged to check whether it was genuine. Hundreds of delegates walked out of Mbeki’s address to the conference in disgust, but many more described themselves as dazed and confused. Over 5,000 researchers and activists around the world signed up to the Durban Declaration, a document that specifically addressed and repudiated the claims and concerns–at least the more moderate ones–of the “AIDS dissidents”. Specifically, it addressed the charge that people were simply dying of poverty:

The evidence that AIDS is caused by HIV-1 or HIV-2 is clearcut, exhaustive and unambiguous… As with any other chronic infection, various co-factors play a role in determining the risk of disease. Persons who are malnourished, who already suffer other infections or who are older, tend to be more susceptible to the rapid development of AIDS following HIV infection. However, none of these factors weaken the scientific evidence that HIV is the sole cause of AIDS… Mother-to-child transmission can be reduced by half or more by short courses of antiviral drugs â€¦ What works best in one country may not be appropriate in another. But to tackle the disease, everyone must first understand that HIV is the enemy. Research, not myths, will lead to the development of more effective and cheaper treatments.

It did them no good. Until 2003 the South African government refused, as a matter of principle, to roll out proper antiretroviral medication programmes, and even then the process was half-hearted. This madness was only overturned after a massive campaign by grassroots organisations such as the Treatment Action Campaign, but even after the ANC cabinet voted to allow medication to be given, there was still resistance. In mid-2005, at least 85 per cent of HIV-positive people who needed anti-retroviral drugs were still refused them. That’s around a million people.

This resistance, of course, went deeper than just one man; much of it came from Mbeki’s Health Minister, Manto Tshabalala-Msimang. An ardent critic of medical drugs for HIV, she would cheerfully go on television to talk up their dangers, talk down their benefits, and became irritable and evasive when asked how many patients were receiving effective treatment. She declared in 2005 that she would not be “pressured” into meeting the target of three million patients on anti-retroviral medication, that people had ignored the importance of nutrition, and that she would continue to warn patients of the sideeffects of anti-retrovirals, saying: “We have been vindicated in
this regard. We are what we eat.”

It’s an eerily familiar catchphrase. Tshabalala-Msimang has also gone on record to praise the work of Matthias Rath, and refused to investigate his activities. Most joyfully of all, she is a staunch advocate of the kind of weekend glossy-magazine-style nutritionism that will by now be very familiar to you. The remedies she advocates for AIDS are beetroot, garlic, lemons and African potatoes. A fairly typical quote, from the Health Minister in a country where eight hundred people die every day from AIDS, is this: “Raw garlic and a skin of the lemon–not only do they give you a beautiful face and skin but they also protect you from disease.” South Africa’s stand at the 2006 World AIDS Conference in Toronto was described by delegates as the “salad stall”. It consisted of some garlic, some beetroot, the African potato, and assorted other vegetables. Some boxes of anti-retroviral drugs were added later, but they were reportedly borrowed at the last minute from other conference delegates.

Alternative therapists like to suggest that their treatments and ideas have not been sufficiently researched. As you now know, this is often untrue, and in the case of the Health Minister’s favoured vegetables, research had indeed been done, with results that were far from promising. Interviewed on SABC about this, Tshabalala-Msimang gave the kind of responses you’d expect to hear at any North London dinner-party discussion of alternative therapies.

First she was asked about work from the University of Stellenbosch which suggested that her chosen plant, the African potato, might be actively dangerous for people on AIDS drugs. One study on African potato in HIV had to be terminated prematurely, because the patients who received the plant extract developed severe bone-marrow suppression and a drop in their CD4 cell count–which is a bad thing–after eight weeks. On top of this, when extract from the same vegetable was given to cats with Feline Immunodeficiency Virus, they succumbed to full-blown Feline AIDS faster than their non-treated controls. African potato does not look like a good bet.

Tshabalala-Msimang disagreed: the researchers should go back to the drawing board, and “investigate properly”. Why? Because HIV-positive people who used African potato had shown improvement, and they had said so themselves. If a person says he or she is feeling better, should this be disputed, she demanded to know, merely because it had not been proved scientifically? “When a person says she or he is feeling better, I must say ‘No, I don’t think you are feeling better’? I must rather go and do science on you’?” Asked whether there should be a scientific basis to her views, she replied: “Whose science?”

And there, perhaps, is a clue, if not exoneration. This is a continent that has been brutally exploited by the developed world, first by empire, and then by globalised capital. Conspiracy theories about AIDS and Western medicine are not entirely absurd in this context. The pharmaceutical industry has indeed been caught performing drug trials in Africa which would be impossible anywhere in the developed world. Many find it suspicious that black Africans seem to be the biggest victims of AIDS, and point to the biological warfare programmes set up by the apartheid governments; there have also been suspicions that the scientific discourse of HIV/AIDS might be a device, a Trojan horse for spreading even more exploitative Western political and economic agendas around a problem that is simply one of poverty.

And these are new countries, for which independence and self-rule are recent developments, which are struggling to find their commercial feet and true cultural identity after centuries of colonisation. Traditional medicine represents an important link with an autonomous past; besides which, anti-retroviral medications have been unnecessarily – offensively, absurdly – expensive, and until moves to challenge this became partially successful, many Africans were effectively denied access to medical treatment as a result.

It’s very easy for us to feel smug, and to forget that we all have our own strange cultural idiosyncrasies which prevent us from taking up sensible public-health programmes. For examples, we don’t even have to look as far as MMR. There is a good evidence base, for example, to show that needle-exchange programmes reduce the spread of HIV, but this strategy has been rejected time and again in favour of “Just say no.” Development charities funded by US Christian groups refuse to engage with birth control, and any suggestion of abortion, even in countries where being in control of your own fertility could mean the difference between success and failure in life, is met with a cold, pious stare. These impractical moral principles are so deeply entrenched that Pepfar, the US Presidential Emergency Plan for AIDS Relief, has insisted that every recipient of international aid money must sign a declaration expressly promising not to have any involvement with sex workers.

We mustn’t appear insensitive to the Christian value system, but it seems to me that engaging sex workers is almost the cornerstone of any effective AIDS policy: commercial sex is frequently the “vector of transmission”, and sex workers a very high-risk population; but there are also more subtle issues at stake. If you secure the legal rights of prostitutes to be free from violence and discrimination, you empower them to demand universal condom use, and that way you can prevent HIV from being spread into the whole community. This is where science meets culture. But perhaps even to your own friends and neighbours, in whatever suburban idyll has become your home, the moral principle of abstinence from sex and drugs is more important than people dying of AIDS; and perhaps, then, they are no less irrational than Thabo Mbeki.

So this was the situation into which the vitamin-pill entrepreneur Matthias Rath inserted himself, prominently and expensively, with the wealth he had amassed from Europe and America, exploiting anti-colonial anxieties with no sense of irony, although he was a white man offering pills made in a factory abroad. His adverts and clinics were a tremendous success. He began to tout individual patients as evidence of the benefits that could come from vitamin pills – although in reality some of his most famous success stories have died of AIDS. When asked about the deaths of Rath’s star patients, Health Minister Tshabalala-Msimang replied: “It doesn’t necessarily mean that if I am taking antibiotics and I die, that I died of antibiotics.”

She is not alone: South Africa’s politicians have consistently refused to step in, Rath claims the support of the government, and its most senior figures have refused to distance themselves from his operations or to criticise his activities. Tshabalala-Msimang has gone on the record to state that the Rath Foundation “are not undermining the government’s position. If anything, they are supporting it.”

In 2005, exasperated by government inaction, a group of 199 leading medical practitioners in South Africa signed an open letter to the health authorities of the Western Cape, pleading for action on the Rath Foundation. “Our patients are being inundated with propaganda encouraging them to stop life-saving medicine,” it said. “Many of us have had experiences with HIV infected patients who have had their health compromised by stopping their anti-retrovirals due to the activities of this Foundation.” Rath’s adverts continue unabated. He even claimed that his activities were endorsed by huge lists of sponsors and affiliates including the World Health Organization, UNICEF and UNAIDS. All have issued statements flatly denouncing his claims and activities. The man certainly has chutzpah.

His adverts are also rich with detailed scientific claims. It would be wrong of us to neglect the science in this story, so we should follow some through, specifically those which focused on a Harvard study in Tanzania. He described this research in full-page advertisements, some of which have appeared in the New York Times and the Herald Tribune. He refers to these paid adverts, I should mention, as if he had received flattering news coverage in the same papers. Anyway, this research showed that multivitamin supplements can be beneficial in a developing world population with AIDS: there’s no problem with that result, and there are plenty of reasons to think that vitamins might have some benefit for a sick and frequently malnourished population.

The researchers enrolled 1,078 HIV-positive pregnant women and randomly assigned them to have either a vitamin supplement or placebo. Notice once again, if you will, that this is another large, well-conducted, publicly funded trial of vitamins, conducted by mainstream scientists, contrary to the claims of nutritionists that such studies do not exist. The women were followed up for several years, and at the end of the study, 25 per cent of those on vitamins were severely ill or dead, compared with 31 per cent of those on placebo. There was also a statistically significant benefit in CD4 cell count (a measure of HIV activity) and viral loads. These results were in no sense dramatic – and they cannot be compared to the demonstrable life-saving benefits of anti-retrovirals – but they did show that improved diet, or cheap generic vitamin pills, could represent a simple and relatively inexpensive way to marginally delay the need to start HIV medication in some patients.

In the hands of Rath, this study became evidence that vitamin pills are superior to medication in the treatment of HIV/AIDS, that anti-retroviral therapies “severely damage all cells in the body–including white blood cells”, and worse, that they were “thereby not improving but rather worsening immune deficiencies and expanding the AIDS epidemic”. The researchers from the Harvard School of Public Health were so horrified that they put together a press release setting out their support for medication, and stating starkly, with unambiguous clarity, that Matthias Rath had misrepresented their findings.

To outsiders the story is baffling and terrifying. The United Nations has condemned Rath’s adverts as “wrong and misleading”. “This guy is killing people by luring them with unrecognised treatment without any scientific evidence,” said Eric Goemaere, head of Médecins sans Frontières SA, a man who pioneered anti-retroviral therapy in South Africa. Rath sued him.

It’s not just MSF who Rath has gone after: he has also brought time-consuming, expensive, stalled or failed cases against a professor of AIDS research, critics in the media and others.

But his most heinous campaign has been against the Treatment Action Campaign. For many years this has been the key organisation campaigning for access to anti-retroviral medication in South Africa, and it has been fighting a war on four fronts. Firstly, TAC campaigns against its own government, trying to compel it to roll out treatment programmes for the population. Secondly, it fights against the pharmaceutical industry, which claims that it needs to charge full price for its products in developing countries in order to pay for research and development of new drugs – although, as we shall see, out of its $550 billion global annual revenue, the pharmaceutical industry spends twice as much on promotion and admin as it does on research and development. Thirdly, it is a grassroots organisation, made up largely of black women from townships who do important prevention and treatment-literacy work on the ground, ensuring that people know what is available, and how to protect themselves. Lastly, it fights against people who promote the type of information peddled by Matthias Rath and his ilk.

Rath has taken it upon himself to launch a massive campaign against this group. He distributes advertising material against them, saying “Treatment Action Campaign medicines are killing you” and “Stop AIDS genocide by the drug cartel”, claiming–as you will guess by now–that there is an international conspiracy by pharmaceutical companies intent on prolonging the AIDS crisis in the interests of their own profits by giving medication that makes people worse. TAC must be a part of this, goes the reasoning, because it criticises Matthias Rath. Just like me writing on Patrick Holford or Gillian McKeith, TAC is perfectly in favour of good diet and nutrition. But in Rath’s promotional literature it is a front for the pharmaceutical industry, a “Trojan horse” and a “running dog”. TAC has made a full disclosure of its funding and activities, showing no such connection: Rath presented no evidence to the contrary, and has even lost a court case over the issue, but will not let it lie. In fact he presents the loss of this court case as if it was a victory.

The founder of TAC is a man called Zackie Achmat, and he is the closest thing I have to a hero. He is South African, and coloured, by the nomenclature of the apartheid system in which he grew up. At the age of fourteen he tried to burn down his school, and you might have done the same in similar circumstances. He has been arrested and imprisoned under South Africa’s violent, brutal white regime, with all that entailed. He is also gay, and HIV-positive, and he refused to take anti-retroviral medication until it was widely available to all on the public health system, even when he was dying of AIDS, even when he was personally implored to save himself by Nelson Mandela, a public supporter of anti-retroviral medication and Achmat’s work.

And now, at last, we come to the lowest point of this whole story, not merely for Matthias Rath’s movement, but for the alternative therapy movement around the world as a whole. In 2007, with a huge public flourish, to great media coverage, Rath’s former employee Anthony Brink filed a formal complaint against Zackie Achmat, the head of the TAC. Bizarrely, he filed this complaint with the International Criminal
Court at The Hague, accusing Achmat of genocide for successfully campaigning to get access to HIV drugs for the people of South Africa.

It’s hard to explain just how influential the “AIDS dissidents” are in South Africa. Brink is a barrister, a man with important friends, and his accusations were reported in the national news media –and in some corners of the Western gay press–as a serious news story. I do not believe that any one of those journalists who reported on it can possibly have read Brink’s indictment to the end.

I have.

The first fifty-seven pages present familiar anti-medication and “AIDS-dissident” material. But then, on page fifty-eight, this “indictment” document suddenly deteriorates into something altogether more vicious and unhinged, as Brink sets out what he believes would be an appropriate punishment for Zackie. Because I do not wish to be accused of selective editing, I will now reproduce for you that entire section, unedited, so you can see and feel it for yourself.

The document was described by the Rath Foundation as “entirely valid and long overdue”.

This story isn’t about Matthias Rath, or Anthony Brink, or Zackie Achmat, or even South Africa. It is about the culture of how ideas work, and how that can break down. Doctors criticise other doctors, academics criticise academics, politicians criticise politicians: that’s normal and healthy, it’s how ideas improve. Matthias Rath is an alternative therapist, made in Europe. He is every bit the same as the British operators that we have seen in this book. He is from their world.

Despite the extremes of this case, not one single alternative therapist or nutritionist, anywhere in the world, has stood up to criticise any single aspect of the activities of Matthias Rath and his colleagues. In fact, far from it: he continues to be fêted to this day. I have sat in true astonishment and watched leading figures of the UK’s alternative therapy movement applaud Matthias Rath at a public lecture (I have it on video, just in case there’s any doubt). Natural health organisations continue to defend Rath. Homeopaths’ mailouts continue to promote his work. The British Association of Nutritional Therapists has been invited to comment by bloggers, but declined. Most, when challenged, will dissemble.”Oh,” they say, “I don’t really know much about it.” Not one person will step forward and dissent.

The alternative therapy movement as a whole has demonstrated itself to be so dangerously, systemically incapable of critical self-appraisal that it cannot step up even in a case like that of Rath: in that count I include tens of thousands of practitioners, writers, administrators and more. This is how ideas go badly wrong. In the conclusion to this book, written before I was able to include this chapter, I will argue that the biggest dangers posed by the material we have covered are cultural and intellectual.

I may be mistaken.

Why did I bother?

2009-04-06T22:41:00.005-04:00

What a waste of my damn time. People are freaking out over paint chips. [Link is fixed, thanks to Chemist Ken]

"The existence of elemental aluminum and iron oxide leads
to the obvious hypothesis that the material may contain thermite.
However, before concluding that the red material found in
the WTC dust is thermitic, further testing would be required.
For example, how does the material behave when heated in a
sensitive calorimeter? If the material does not react vigorously it
may be argued that although ingredients of thermite are present,
the material may not really be thermitic." [Emphasis mine]

Maybe I'm not reading it correctly, but what does that even mean?

I'm sorry, I'm may be an idiot, but I'm not stupid. I love how they stretch facts through words like "compelling" and "surprisingly". I guess the troofers will have their fun. It isn't really something I spend time thinking about except people keep sending me this stuff. Stop! Please!

Impatience & the Aufbau Principle

2009-04-01T20:27:00.002-04:00

Wolfgang Pauli and Neils Bohr formulated the expression of a rule that governs the chemistry and physics of atoms called the Aufbau Principle. Stated simply, the principle is that elections fill an atom's various orbitals in order of lowest energy to highest energy. They will not add in any other way- i.e. they must "build up". In fact, this is what Aufbau means- "building up" in German.

In a sense, it can be a metaphor for the learning experience. You cannot learn physical chemistry without physics, you cannot learn physics without calculus, you cannot learn calculus without algebra, and so forth. You can of course, but it is more difficult, and ultimately you will struggle for proficiency rather than mastery. I can teach someone to do simple derivatives by teaching them the various rules regarding powers. An eight-year-old could learn that 2x^2 should be rewritten 4x and how to solve simple problems by rote.

I'm happy with what I'm learning now, and after a little bit of hectic discombobulation while I was in catch-up mode due to illness, I'm back to full sails and smooth waters. Still, that's a little boring, and sometimes I find myself very curious about various phenomena that I won't get around to until later classes. I get antsy, in other words. It's okay when it manifests itself in extreme nerd behavior involving studying for next semester, but it's a little sad when I'm in the library at nine o'clock in the evening looking up stuff on a ten year old textbook for something that may be very out of my league. My friends think I'm insane, and I have to agree a little.

It's a sort of stir-crazy: Ultimately, It's a consequence of stasis. I've been in school too long. A late change of major means I'm aching to exit the undergraduate world- without much regard to where I'm headed afterwords. Meanwhile, I'm stuck to going one semester at a time, and things are moving abhorrently slow. It's not a rut, it's not a case of me being down in the dumps. I'm actually quite excited and engaged by most of the material I'm learning. It's just that I sometimes get this inescapable anxiety, similar to the feeling like you're in an elevator that just taking a just little too much time to get where it's going.

Basically, I have to be patient- it's not like I have a choice. Really, the only thing I can do about it is gripe a little. I'm hoping to join up with a lab as an undergrad assistant soon (hopefully sometime after this summer) and that will help immensely. Meanwhile, I'll be attending class after class, building...

Ever Been There?

2009-03-30T21:11:00.004-04:00

Wow, I don't think I've ever been so completely and wholly wrapped up in something like this man. I actually feel envy, not for owning or possessing any object, but for the vibrancy in the attempt to attain it. I don't mean to sound hackneyed, but this is clearly a case where the journey is more important than the destination.

Link Love

2009-03-29T18:39:00.002-04:00

I've been putting off sorting out my blogroll for a good long while now. There are so many good blogs out there, and I fear, so little column space on this particular template. Never fear though. I'm renovating a little around here. You may have noticed that the margins are a little wider. I've tested reading in both IE (Why are you still clinging to the past?) and Firefox, so there shouldn't be any display issues.

Regardless, there are a few good websites out there I feel should at least get mentioned on this blog once, if not permanently blogrolled. The websites I have not previously linked, but meant to, follow below.

Science-Related:

The Curious Wavefunction- A blog I follow, but for some reason never got around to blogrolling. Shame on me! Ashutosh frequently blogs chemical literature with great acuity. Quality of posts in consistent (something I can't say for this blog) Science-related political posts are always insightful and I tend to learn things when I read the blog, a bizarre and unintended consequence.

Cosmic Variance- I have a reputation for being a little spaced out. Perhaps this is why I find astronomy fascinating as a subject I have no intention of specializing in. More importantly the writing style of this blog's various authors. Topics range from space, physics, and science to the current financial crisis. Always worth a look.

Chemical Dependence- Food. Science. Really, what more is there? I'm always appreciative of any website that makes me hungry with pictures of food. The fact that it's run by a chemist is a plus. Don't go defunct on us though!

Observations of a Nerd- I just came across this the other day, and it's actually a very well written blog, considering it's written by a biologist with the temerity to minor in chemistry. Ah, well- no one's perfect. I actually believe I still owe her a small plush toy.

Other:

Sinfest- Is a great example of how something charming and pretty innocent can be denied entry into the mainstream because it casually references sex, drugs, and religion. Syndication has been an issue for the cartoonist, Tatsuya Ishida, and I doubt it will find it's way into your local daily anytime soon. Anyone want to ask why old media is dying again?

NOOOO!

2009-03-19T00:01:00.001-04:00

Really?

Transparent Sodium

2009-03-18T19:15:00.004-04:00

From ScienceDaily, by way of the Bad Astronomer:

"An international team of scientists have discovered a transparent form of the element sodium (Na). The team, led by Artem Oganov, Professor of Theoretical Crystallography at Stony Brook University, and Yanming Ma, the lead author and professor of physics at Jilin University in China, was able to demonstrate that sodium defies normal physical expectations by going transparent under pressure."

It's always fun to do new things with metals, including turning them transparent. This isn't making transparent metal compounds and calling it "transparent aluminum" either. It's quite remarkable. Apparently, the pressure (~3 Mbar) forces electron localization, making the sodium lose some of the principle characteristics of metals. Abstract is here (doi:10.1038/nature07786) If link is faulty, let me know.

Happy (Belated) Pi Day!

2009-03-15T23:44:00.004-04:00

I missed pi day! What an almost unforgivable lapse. Here's a cool pi related video. Funny, pi day falls on a Caturday and icanhascheezburger has got nothing? That's messed up.

I wonder if the same person does the LHC rap.

Syringe Cringe

2009-03-13T16:44:00.003-04:00

I had a most unexpected mishap in the lab today. Gas chromatography, a method used by chemists to analyze the purity or relative makeup of substances (among other things) is not something I generally consider fraught with hazards. You can burn yourself touching the wrong side of the machine, since it has a built in oven, but generally I see no reason for any more caution than say- watching a movie on your computer while sewing a button onto a jacket. The sewing part has to do with the fact that using this particular (and common) gas chromatograph involves injecting a sample with a long thin needle past a rubber barrier.

No I did not inject myself with the needle. I'd have to be a complete yutz for that. Actually what happened was a little more surprising, and I'm sure I'm just lucky this hasn't happened before. For the non-chemists out there, a gas chromatograph uses helium as a carrier (I'm going to try to explain chromatography in a later post) and the injection site has some positive pressure. Normally I don't give this a second thought, in fact, it never occurred to me. So instead of injecting the substance right away, I left the syringe in while I found my pen to make a quick note. When I turn back to the syringe, the positive pressure pushed out the plunger and sprayed me in the face with foul liquid. I'm extremely grateful my mouth wasn't open at the time. Even thought the syringe only holds a few microliters (1 milliliter is 1000 microliters), the stuff was atomized quite nicely and was made of pure nasty. The stuff positively reeks, and getting hit square in the nose was- in a word, unpleasant. This is the first time I've had to wash my face in a lab. The smell itself was all sorts of sticky-sweet, flowery wretchedness.

I don't know what exactly was in the sample, before you ask, at least I haven't got around to it yet. It's malodorous nature screams "ester", though. My misery did get a little company though. I called over one of the TA's to help me out, because the machine wasn't cooperating, and she loaded the syringe up with acetone for a test run- only to have the exact same thing happen to her. Acetone is a lot less nasty though and evaporates virtually instantly. I'm just glad I'm an undergrad and they don't trust us with anything really nasty yet. (Well, if by glad, I mean slightly disappointed.)

Rep. Conyers, Please Step Aside.

2009-03-11T15:09:00.004-04:00

This was recently brought to my attention through the Bad Astronomy blog by the astronomer Phil Plait. Representative Conyers (D-MI) wants to make it impossible for federally funded scientists to publish papers except in scientific journals, and specifically ban open access. In other words, that NIH study you payed for with your tax dollars? Yeah, you're going to need a subscription to the journal it was published in to read it. Phil Plait has details here and here, and I've taken this video featuring Lawerence Lessig from Phil's blog and embedded it below. Ed Brayton has written an excellent article here as well.

Victory is Phil's!

2009-02-20T10:17:00.003-05:00

Over at Bad Astronomy, Phil Plait's latest post is a video explaining the importance of science. It's part of a larger project called "Why is Science Important?" Scientists make videos describing why they think science is important. It kind of gets back to a post Ashutosh left on The Curious Wavefunction, discussing the way science is presented to the public. My comment was that scientists should do their own PR- and what better way than this? Phil Plait has a great engaging style- and a poster featuring Stewie Griffin, so I think he's great for this sort of thing.

My one criticism of his video is the way he focuses on technology to represent the importance of science. I've never really felt technology was the raison d'etre for good science, it's simply the raison d'etre for private companies' R&D departments. Not that there is anything wrong with technology, of course. I tend to think of science as being on the same level as art. Pre-agricultural humans spent fewer hours working than modern humans. Modern humans don't work continuously in a toil to preserve their existence. It's unnecessary, and what's the point of existence if it is simply to exist?

Meanwhile, we laugh, we love, we play darts, and we explore our worlds and our lives. Is it so wrong to suggest that man should seek his own pleasure among the stars, and on Earth? That the joy of exploration is reason enough? Why is it that we devalue anything that does not have a place in the paradigm of industrial production? I argue that science has a place beyond technology, because humans have a place beyond mere existence. Ever since we were leaving paintings on cave walls, it has been in our nature to revel in our humanity, and discovery will always be part of that legacy.

Why Hitchens Is a Hack

2009-02-19T22:07:00.002-05:00

Hitchens is to me, one of those people like Ben Stein. Someone who stumbled into the spotlight and was kept there by only the faintest whiff of scholarship. This episode describes part of his unmitigated failure to at least have enough subject knowledge to back his arrogance,

"In order to illustrate how he knows so much more about Lebanon than anyone else in the room, when pressed, the only “true revolutionary” he could come up with was Walid Joumblatt. To this, the audience mostly just laughed out loud. I would have felt sorry for Hitchens if he hadn’t been such a pompous ass."

Walid Jumblat (وليد جنبلاط) is a damn sleazeball opportunist, among other things. An equivalent would be asking a [Insert random nationality here] who he admired on the American left and having him reply, "Rod Blagojevich."

Meanwhile, I will never cease to be amazed that there are still people out there who admire this man.

A Good Science Article. No... Really.

2009-02-17T15:19:00.002-05:00

A science article by someone who understands science! Holy crap, finally! God only know the number of POS articles that appear in health sections of newspapers and magazines that promise antioxidants will cure you or that plastic bottles will kill you. I would go so far as to make this article a must-read in every high school. Very few people understand that scientists don’t perform studies to achieve newspaper headlines (okay, well some probably do), but by and large they are working incrementally towards answering a larger questions, publishing the results of the lesser questions along the way. Meanwhile, their research could be flawed or preliminary.

An important take-away message from this article is the scientists miss things sometimes, and when dealing with complex multi-variable phenomena they are especially prone to overlooking a key variable. Even the best and the brightest have had their ideas ruthlessly shot down. Right now I’m reading James D. Watson’s autobiographical book, Avoid Boring People: Lessons from a Life in Science. This was the man that co-discovered the structure of DNA. Long before this ever happened though, he writes about being a graduate student who had his some of his research findings on phages eviscerated by no less than Leo Szilard- who switched to biological experimentation after World War II.

I wish the author of the article would have had the time to go into statistics and significance. A good introductory book on the subject is the classic How to Lie with Statistics, by Darrel Huff (which also manages to be a really good read). It may have gone over the heads of a lot of readers but it’s something that I think more people should be familiar with. If for no other reason than it helps them to identify when someone is lying that someone else is lying with statistics.

UPDATE: It might help if I actually link the article I'm referring to. Oops.

Don't Be A (Boron)*

2009-02-14T23:41:00.001-05:00

I stole this from CBC, which makes it kind of pointless to post, since they may be my only readers:

*Yes, that was the best joke I could come up with.

Go Watch GPB NOW!

2009-02-10T21:11:00.001-05:00

If you live in GA, and you're reading this shortly after I've written it, switch over to Georgia Public Broadcasting, Nova's doing the story of chemist Percy Julian.

If you don't live nearby, check your local schedule. This might be a rerun, I don't know, it was a welcome surprise to me while flipping channels.

Atlanta Skepticamp '09 is here!

2009-02-05T00:42:00.002-05:00

For those of you in the Atlanta area, may I present: Skepticamp '09.

I have no idea what it's going to be like, this being the first one and all. See the main page or the Facebook group for more. I'll definitely be there. I'm just disappointed I found out about it so late. I might have convinced someone to come give a talk about chemophobia and the recent "detox" movement. So if you're in the Atlanta area this weekend, see if you can swing by.

Double-Take

2009-02-05T00:03:00.002-05:00

Sometimes, as a scientist in-training (when do I get to call myself a scientist?) I see things on television which are utter nonsense. I'm not talking about things like flashing bullets, or gasoline explosions where special effects are an obvious assault on the natural laws of the universe. Sometimes though, there are real head scratchers in a movie or tv show which you can't really call bad science because the characters are dealing with sci-fi concepts not actually based on anything we understand.

For example, I sat up a little straighter in my seat when I was watching The Fantastic Four for the first time on television. I saw the scientist of the group working on a blackboard with an intense focused look on his face as he pondered the mysteries of his mutations. On the actual board however was a mundane equilibrium calculation on it. I don't remember what it was, all I know was that it looked like something ripped out of a high school textbook. Simple equilibrium calculations of this nature are pretty mundane, and while they are used for some things, it's not really the sort of thing that requires intense thought. There was nothing wrong with the equation that I could see fleetingly, it's just that I can't imagine how it would be useful in that context. This is the sort of thing I'm talking about. Things in movies that are more "sciencey" than scientific.

Then, yesterday I was watching Fringe. Now I swear I don't watch sci-fi just to point out all the errors, but there are some things that make complete suspension of disbelief impossible. There's a part where I see one of the characters pouring some thick green liquid into a rotavap. Yes, into the actual rotavap, in the vaccum column. It was a fleeting cut, so I may have misinterprested what I saw, but I'm pretty sure I actually saw the character pouring crap into the vaccuum column (not the coils either).

I cannot imagine for one second why you would do this on the one hand. On the other, people improvise lab equipment all the time, and the whole point of the show is that the science being dealt with is "fringe". I can't really say that it defies science as we know it, all I know is that the prop department potentially ruined a perfectly good rotavap with green paint.

Science Secret

2009-01-22T17:24:00.003-05:00

If you've never heard of Post Secret, you've been living under a rock.

I knew a guy who used to steal reagents from lab back in high school. It would be stuff like magnesium strips so he could ignite home-made thermite- nothing big. I myself have taken something from the lab before, but by accident. It was one of the few days I was wearing a lab coat and I had taken a few of the disposable Pastuer glass pipettes in back home with me in one of the pockets. Thankfully they didn't break when I bunched it up in the bottom of my bag, which is some kind of miracle.

I actually want to buy a series of erlenmeyers diminishing in size down to a 25 mL one and set them up on a shelf at home matryoshka style. It's still not illegal to own erlenmeyers in Georgia, though you need a permit to buy them in Texas (everything is more ridiculous in Texas).

My Conversion Story, Continued...

2009-01-19T13:25:00.007-05:00

Well, I said in my last post that I might soon be posting using the power of the penguin. Well, I was right to expect that installing Fedora (Yes, I changed my mind yet again) would be easy, I just had no idea how easy it would be. The whole thing was gravy. When I install XP, I have to install all the drivers just to use the Internet. In this case, my wireless card was detected right away and Firefox was already sitting on the taskbar. I still had to tinker with a few things, but the issues were fixed in a matter of seconds.

The GUI bears some similarities with Macs, and because both Mac and Linux are UNIX-based, so does the filesystem. I was raised a good MS-DOS kiddie by my father since my first computer, and opening up the terminal, find this new shell very foreign. Many of the commands I was used to no longer work, and it's strange to have to enter the root password to access parts of the filesystem, but it's obvious how much more secure it is. I'm revelling in my new-found immunity to Windows viruses/worms/exploits/cracks and the large community of bothersome script-kiddies.

I'm still getting used to using shell commands, and Fedora 10 has some known issues with my particular graphics chipset. It makes rendering in Firefox a little sluggish and wonky. There's a fix, but frankly, it's a not a big enough nuisance that I'm in a hurry to try it right away. Worst case scenario means I have to rebuild my driver from the bottom up, but I don't think it will come to that. Beyond that, any issues I've had with Fedora are purely ones of orientation. I still am not quite so comfortable kicking around the system.

I did find everything I needed to get work done on my system though. I can read and write Word documents (though I should probably find a reader for the new office formats). It comes with OpenOffice.org, as well as some fun stuff, like DOOM. (You have to unpack these from Add/Remove Programs) It even has LaTeX and TeX installations ready for you should you want it. Sure it's easy enough with Windows, but I like an operating system that knows what I like. (Yeah, as an undergrad I don't really find as much occassion to use it, but I like having it anyway.)

One application that I'm going to find useful is Alexandria Book Collection Manager. I was thinking about making a database or a quick and dirty VB or VC++ app, but I never got around to the task, now I guess I don't have to. (Thank God, I would have had to learn VB or VC++, ugh)

The GIMP comes installed, which beats MS-Paint into the ground and steals its lunch money. I even used it back when I had Windows, even though I was still a Paint fiend when I needed quick and dirty diagrams. That was mainly because I wasn't all too sure how to use GIMP but like other Linux issues I find it's simply a matter of adjustment.

The one thing about Linux, and really the only thing, that makes me raise an eyebrow, is complicated installation of programs and add-ons in Linux. I'm not used to being so involved in the installation at the shell level, and you don't ever see that in Windows. There HAS to be a way around that, even if only through reprogramming the kernel. Oh, I'll do it if I have to. (No I won't)

All in all, I have to say I'm a fan. There's really no reason so far for me to go back to windows. Sure, I like playing computer games, but I already have a video game console. Meanwhile, so long as I can play ~~Tetris clones~~ Powder (Warning: addictive) on my PC, I'm okay. Suck it Winblows!

Logical Conclusion

2009-01-18T15:22:00.003-05:00

I hate Windows, am wary of Macs (not to mention not ready to buy a new computer). There is only one logical thing for me to do:

Yes, I will be installing Linux on my computer. After verifying that everything I want to do, I can do with Linux, I have decided to install Linux on my Crapomatic. "Crapomatic" being my old HP which I'm using while my other computer is being repaired. It has a one pixel wide streak running down the right side of the screen and has no keycaps on the "f" or "j"keys. I have nothing to lose, and potentially quite a bit to gain.

I'm installing ~~Fedora~~ Ubuntu (changed my mind), I have the Debian and Ubuntu distros on CDs as well. I've downloaded all the Linux hardware drivers I could get my hands on, as well as the Linux versions of Firefox, DivX, and other popular apps. I'll let you know how it goes. Next time I post, I may be using the power of the Penguin.

Corny

2009-01-13T14:35:00.006-05:00

Kewl. How'd they do it?

I just want to slap a big "Citation Needed*" on it, but if they're compostable, they're compostable. I'm thinking of using it as a flowerpot and seeing what happens. Add some coffee grounds, and I'll have a thriving environment for a petunia, or what are some cool plants to grow? (Yes, it is in fact filled with ice-water)

*Oh, I'm still pissed at you Randall. Don't think I'm letting you off the hook.

A Quick Lament

2009-01-09T18:46:00.002-05:00

Why is it that after class, whenever I want to ask a professor two questions: A smart question and a dumb question, by the time they turn from answering another student, I can only remember the dumb one?

Just to preempt the old saw, I am aware there are no stupid questions, only stupid people.

Im in Ur Labs- Arresting Ur Colleagues!

2008-12-29T04:36:00.003-05:00

It never gets old does it? It seems like if you follow this sort of thing, it happens every other day. Every other day some chemistry student, some sixteen year old, even a professional chemist with decades of experience is arrested or raided because the police think they have a meth lab. Well, I submit for your disapproval: The exact same thing all over again.

I'm really at a loss for words here. How can you describe the level of vapidity and ignorance on the part of the police? This is an absolutely disgusting extension of the War on DrugsTM (or whatever version of it they happen to have up there in Canada. To be frank, even if I felt that the WoD was absolutely justfied- which I don't- I would never give police carte blanche to do anything whatsoever. As far as I'm concerned, authority figures shouldn't be able to scratch their asses without a warrant.

Someone needs to drill it into these idiots' heads: Science is a verb. You perform it. It's something that is taught as a practice, and frankly- in terms of getting certain substances or achieving certain effects, skilled chemists don't give a shit about your silly pointless restrictions on chemicals. We can work around them- it's what we do. Getting what we want from what we have available has been one of the main missions of chemistry ever since its practitioners were called alchemists.

If you're interested in helping the overall situation (since I can't find a defense fund for Lewis Casey) consider making a monetary donation here (I know I did, and I rarely ever do). This happened in Canada, so I can't exactly call a congressperson up in the US. However, I don't think scathing (yet polite) letters of rebuke to the Saskatoon Police Service are entirely unwarranted or uncalled for. It probably won't help, but you'll feel better.

Tip of the NI3 soaked cap to PZ Myers who summarizes my frustrations quite nicely.

"You done picked a fight with the wrong crowd!"

2008-12-22T16:58:00.005-05:00

XKCD has taken sides. It's on now. It's on like Donkey Kong!

(Click for enlargementation)

I sorry, but Randall Munroe is officially not invited to come to any of our cool parties.

Bah! Cuttlefish... what is it that takes care of them? Salt was it? Or was that for slugs? Screw it, habitat destruction. Suddenly, I think I know what we should do with all of our industrial waste.

Grades and Knives

2008-12-21T16:02:00.004-05:00

So grades came out for this last semester- turns out, despite my bad showing at the end, there I came out relatively unscathed. I was expecting a couple of Cs but in the end I walked out with B+s and As. So I wasn't as affected as thought. I have to remember to pick up a souvenir for my professor though, one of them in particular has a variety of trinkets from students who have been abroad. I'm not sure what to get him, but I'm thinking a traditional Emirati khanjar might be nice. A khanjar is a traditional curved dagger, once carried by every desert nomad, now superseded by the cell phone, which is the khanjar of urbania I suppose. Nowadays their sole purpose is to be decorative, and have pleasantly ornamented scabbards and are meant to be hung on walls. I have my own khanjar, though this was from Yemen where it is called a jambiyyeh. It's somewhere in storage, unfortunately.

Like I said, mine is somewhere in storage, so this image comes from Coyote's Paw.

Here in the Emirates it's not worn, but in Yemen it is still worn by many as an accessory. However it's generally considered taboo to unsheathe it in public. I personally prefer hanging it on a wall. Another possible souvenir for my professor is a traditional Arabic coffeepot. These are actually featured on the money in this country:

Image from Wikipedia: With this, you may purchase a can of coke. It's about 28 cents. Go figure that out the next time you're at a vending machine.

Coffee is an important part of traditional social customs here. I'm not such a big fan of Arabic coffee though, everyone tells me it's really bitter/strong. Even people who positively hate the stuff tell me this. I personally think it tastes like nothing- boiled water. I really don't detect any taste. As such I can't say I love or hate it, it just is. Turkish coffee on the other hand, I love, and I have yet to taste anything stronger. It's a lot more common here- you can find it in most cafes.

Pretty much anything would catch the interest of my professor in this case, and I'm not too worked up about it, but I've always found it difficult to assess the relative value of souvenirs. I mean, think about it, knives and coffeepots are pretty much household items. I wonder if people in the future will ever see that sort of thing as a matter of cultural heritage.

"And here, we sell the old-fashioned Wii. A long time ago, people used to stand in front of these big boxes called televisions for entertainment (this was before brainfeeds) and used it to play primitive games. I can sell you separate stands for the controllers if you don't want to mount them."

Can You Say "Faux Pas" In Mandarin?

2008-12-06T19:24:00.002-05:00

The Max Planck Institute, for those unfamiliar with it or its namesake, is a respected scientific research organization. Recently, they made an embarrassing error that should have and could have been avoided.

Was it an issue of scientific integrity?
Was it a retraction?
Was it a tacit endorsement of psuedoscience?

No to all. It turns out that the MaxPlanckForschung, their journal, doing a special edition on China, printed an ad for a strip club on the cover, instead of what should have been a Chinese poem. Their response to discovering the mistake:

Dear Colleagues,

The cover of the most recent German-language edition of MaxPlanckForschung (3/2008) depicts a Chinese text which had been chosen by our editorial office in order to symbolically illustrate the magazine's focus on "China". Unfortunately, it has now transpired that this text contains inappropriate content of a suggestive nature.

Prior to publication, the editorial office had consulted a German sinologist for a translation of the relevant text. The sinologist concluded that the text in question depicted classical Chinese characters in a non-controversial context. To our sincere regret, however, it has now emerged that the text contains deeper levels of meaning, which are not immediately accessible to a non-native speaker.

By publishing this text we did in no way intend to cause any offence or embarrassment to our Chinese readers. The editors of MaxPlanckResearch sincerely regret this unfortunate error and would like to offer an unreserved apology to all of their Chinese readers for any upset or distress they may have caused.

The cover title has already been substituted in the online edition, and the English version of MaxPlanckForschung (MaxPlanckResearch, 4/2008) will be published with a different title.

We would ask you to forward this information to all Chinese scientists at your Institute. Please find attached the new version of the title. Perhaps you can distribute this print-out within your institute.

Oops.

Tip of the jade-like hat in the spring of youth to Fark.

So Gay.

2008-12-05T14:01:00.003-05:00

Enjoy this little ditty, I haven't seen Niel Patrick Harris sing since Doctor Horrible's Sing-Along-Blog, but it's getting to be a treat.

Perfect!

2008-12-01T20:25:00.002-05:00

"So, you have an end of semester assignment to complete do you?" Your computer asks.

"Yes, as a matter of fact I do, it's great though because I have most of it done- now I can spend most of my night completing other assignments."

"Okay. I'm going to crash now."

*FOOM*

Yes friends, my hard work has gone up in smoke. I turned on my computer, and shortly after logging on, it decided to put up a blue screen of death for like a nanosecond before restarting. It won't let me do shit now. At first I though this might be a hardware issue, since having my LAN cable inserted seemed to exacerbate the issues. This prospect scared the hell out of me. I though it was some bizarre electrical short. I once got a good minute in before the automatic restart and
sneezed- and everything promptly shut down. It's just post hoc ergo propter hoc though. Something really fucked with my system files. know all my data is still there safe and sound, and I have a partition- so I can reinstall windows if I have too.

My strong suspicion is that my computer has a virus. Normally I'm very good about where I go online. I even have a second user account that I can go into that has maximum security settings in case I decide I might want to do something risky. The other day though, I stumbled upon one of those weird icky sites. You know the kind, badly designed, almost 100% ads, and does weird things with windows resizes.

It's going to be a long night, and tomorrow I have to head over to the polling place after class so I can vote in the run-off election here in Georgia, then I have to worry about getting plane tickets for my brother and I for the holiday, a check not depositing to my account for some reason, a final on Wednesday, and tons of reading. None of this is entirely unexpected, but the computer thing really fucking bites considering how much I need it right now.

Gobble Gobble

2008-11-27T12:11:00.002-05:00

Happy Turkey Day!

Celebrate by looking at this drawing of a tryptophan molecule:

Now regale your friends and family with the fact that it doesn't make them sleepy. That would be the eating-a-third-of-your-bodyweight-in-carbs thing.

I ♥ Consumer Reports

2008-11-25T17:41:00.005-05:00

Consumer Reports is not frequently seen as scientific or skeptical, but I beg to differ. I can't speak for the whole chemical community but it's fair to say that it is sometimes frustrating to see how "natural" products market themselves when they are chemically identical to their synthetic versions. Just because you made it from corn and made food prices go up, it doesn't change the fact that the stuff in the green bottle is the same as the "nasty chemicals" in the red bottle.

We call this chemophobia, a fear of chemicals created by ignorance of basic chemistry. Sometimes this fear is rational: I've gotten a chemical burn using drain cleaner before, and generally you want to use powerful oxidizers, reducers, acids, and bases carefully. "Chemicals" is a broad class. The set includes everything from the innocuous and everyday (Water) to the horrific (thalidomide). Yet we can drown quite easily in water, and thalidomide has shown utility for some conditions in men. Deferring to the process of science is the only way to truly assess the risks and benefits of the world around us.

Minor Clarification: The CR posting makes clear that we don't know for sure of the "green" stuff in question is necessarily chemically identical to the original. I just wouldn't put it past them. For some products I've seen, the level of deliberate honesty is akin to slapping "fat-free" labels on bags of sugar. (Makes mental note to try that.)

Infuriating

2008-11-22T18:49:00.003-05:00

Okay, so the gays totally suck and can't get married. Meanwhile, schools are taking out ads on tests so they can afford to print them. Good to know our government has its priorities straight.

This is disturbing on more than one level. Schools should not be run like businesses. I blame the "tax & spend" slogan for this. As a society we seem to have collectively forgotten that taxes are not in fact for punishing people for no reason, but that taxes actually serve to fund very real and essential public services. Instead we have immature arguments whereby any amount of taxes seem unnecessary and burdensome. This is not a case where the teachers and students should simply be happy. This is a case where the community really needs to take a long hard look at the budget and work things out competently. The parents should be making a big deal out of it.

The article says there's been no complaints so far. Good. Don't come crying to me when your children have golden arches on their school uniforms so they can "pay" for their education by making fries after school.

Stupid.

2008-11-15T11:52:00.003-05:00

Via Fark: Read this silly story on loyalty oaths.

How about we cut them out as a "tradition" altogether? It serves no purpose and only makes people uncomfortable. Why do we have to enforce this sort of thing?

It's a ridiculous and antiquated prayer ritual that started in 1892, and espouses the mythology of America rather than the reality.

AP: Russian Sailors Fell to Freon Poisoning

2008-11-09T09:51:00.008-05:00

Twenty Russian sailors died during a non-nuclear incident aboard their nuclear submarine. Apparently they were essentially gassed by their fire suppression systems when they went off by accident. The article I read mentions that they were poisoned by Freon gas.

Freon is word you may recognize as being an important chemical in the refrigeration and air-conditioning industries. Despite its potential for ozone depletion, it remains in use. In fact, every house I've ever been in with air conditioning has used Freon. More on that in a second.

What's In A Name?:

At this point, I should clarify that Freon is a trade name used by Du Pont to describe a class of chemicals known as haloalkanes. Your know that Tylenol is simply the trade name of one company's acetaminophen, for example. So what's a haloalkane. Well, let's start with the last part of the word.

An alkane is any simple organic molecule that is primarily comprised of carbons attached to each other by single bonds. A double bonded carbon in the molecule would make it an alkene. All alkane carry the -ane suffix, just all alkenes carry the -ene suffix. So we have butane and propane pictured below:

The "halo-" simply means anything from the Halogen group on the periodic table, Group 17 (or on some older tables, Group 7A or Group 7). They are: fluorine, F; chlorine, Cl; bromine, Br; iodine, I; and astatine, At. Each of these has a valence of one, meaning they can have one single bond at a time. Now look back up at the alkanes, you'll notice that hydrogen can only bond once. Replace any or all of the hydrogens with chlorine atoms, for example, and you have yourself a simple haloalkane.

When you add fluorine to this molecule, it becomes a chlorofluorocarbon, which is still a haloalkane (remember fluorine is a halogen too.) Then you get the handy acronym we are all familiar with:CFC.

The Freon that caused problems on the Russian sub was probably from a class of fire retardants called halons. Halons can kill you at high enough concentrations, and a submarine is a bad place to be if you need to escape toxic gases. UPDATE: The BBC has reported it was a case of asphyxiation, as opposed to direct toxic effect. I suspected this might be the case, as has a commenter, but that's not the way it was reported.

Image from Wikipedia

EEEK! This Stuff Is In My Air Conditioning. PANIC! PANIC! PANIC!:

Freon is also in you refrigerator, but it's not time to panic. First of all, like I said, Freon is a trade name that describes many different chemicals in the same class. The Freon in your home is non-toxic, and that's a major selling point. Before Freon, the stuff we used as refrigerants were toxic. This included things like ammonia, sulfur dioxide, and methyl chloride. A refrigerator leak could be downright dangerous.

----------------------------------
However, as Baum pointed out in the comments below, chances are your newer AC and fridge are not using CFCs, but HFCs or another compound. I've personally been using older stuff, so I forget to mention that the new stuff getting churned out of factories is CFC free, except for Russian products. They still use it in spray cans. Other countries may also be putting CFCs where they don't belong. See below.
----------------------------------

So it's not time to throw out your fridge unless you want to save the ozone, which coincidentally is also technically toxic. Actually, CFCs are technically banned globally. So why do you still see them?

"Psst! you wanna buy some Freon?" The Illicit Trade in CFCs:

News that sounds like a joke: The illicit trade in CFCs is second to cocaine as an illegal import. At least according to Joe Schwarcz, chemistry professor at McGill University. The Montreal Protocol of 1987 allows for stockpiled and recycled CFCs to be used in North America. Older refrigerators and AC units still run on CFCs and must be periodically maintained with this amount. However, countries like Mexico and China are permitted to produce until 2010, and import their wares with false recycled certificates. According to Schwarcz, the Russian Mafia is also making a racket of of this.

I'm waiting to see what will happen in 2010, when many of these sources are no longer permitted to operate.

Oh My Stars and Garters...

2008-10-29T10:37:00.010-04:00

It was a long time ago that I stumbled onto Dr. Phil Plait's website, Bad Astronomy, which I found after searching for a review of the movie The Core. Ever since then I have been reading his blog regularly, and I even went out and got his book. His first book, Bad Astronomy, was a collection of misconceptions and mistakes propagated about space and by extension, physics. For anyone who knows someone who believes in the moon hoax, I highly recommend it. Now he has written a new book, called Death From the Skies.

I went out and bought it, having waited for it ever since Phil began pimping it on his blog. It's a book that goes over the number of ways things outside of earth's sphere can kill us. I know that "things outside of the earth's sphere" technically means space, but let's face it, it's not the void that going to kill us, it's the stuff inside the void [/nitpick]. Provided we don't manage to do the job ourselves, the book points out that the earth will be destroyed eventually, in some scenarios sooner, rather than later. The book's cover (pictured below) has a great movie poster look to it alright, but the really good stuff lies beyond the dust jacket.

ORLY?

As you might imagine, a book about how the earth will end is largely speculative, but there are some interesting things to contemplate. While unlikely, what exactly would happen if a black hole suddenly showed up in our solar system and headed straight for the earth? Allow me to sum up the crux of Plait's conclusion: We die.

However that short sentence doesn't do Phil Plait's explanation justice. What he does, is go over it all in brilliant detail, explaining the strange and elegant physics of this hypothetical event. There is something about his writing, a quality I find difficult to describe, that makes everything abundantly clear very quickly. He doesn't seem to struggle to explain things, and every thing is usually transparent to the reader.

In fact his description of the death of a star made it easy to imagine a perspective from a seat inside the star watching in awe as the scaffolding falls around you. His descriptions, sometimes rather poetic, bring life and color to that deep black void in our minds that we normally reserve for space.

To be clear, it's not a perfect book. It's great, certainly, but there were some improvements that could be made. For one there was a typo I managed to catch- a minor one where he states about the bending of space, "It's actually incredibly difficult to describe the shape of the space being bent because we live in those dimensions..." I'm pretty sure he meant because we don't live in those dimensions. [Edit:There is no typo, I misunderstood the intent of the statement. Sorry.]

Aside from that minor typo, which isn't really a criticism more than it is a testament to how difficult it is to churn a book out without errors, there are two other items. He has some amazing images in the book, some of which I assume are artistic renditions, but are amazing nonetheless. Tragically, none are in color, and they lose quite a lot of their potential impact. Plait should know something about potential impacts, hell, the book is full of them! It was probably a decision based on the cost of printing in color and the sale price of the book, which I was foolish enough to buy from the bookstore instead of Amazon. What can I say? I don't like to wait, and I payed the tax.

My final criticism: The book is too damn responsible. It tries so hard not to start a panic that it gets to be a little old. I get it. The sky is not in fact falling. I like that he goes over the low odds, but it sometimes snaps me out of my apocalyptic fantasy. I approached the book like a horror story, it doesn't get you good and scared more than you get yourself good and scared. It's hard to watch a movie like Halloween and have the Micheal Myers character constantly pull off the hockey mask and remind you, "I'm just an actor!" Of course I understand the need to express the likelihood of the various events, but this is a case where less just might be more.

Beyond that I highly recommend it, and it should be a pop-science staple. It's really very much in the same league of astronomy books that make you realize not only your littleness, but the majesty all around you. The title of this post- if you're a comic book fan you might recognize it- comes from the X-Men character, Beast. It's his trademark exclamation. Well, I came across its possible origin a while back and it kept popping into my head. From Hans Christian Anderson:

"It’s really a pleasure now and then to become a mere nothing, especially when a man is as highly placed as I am. And then to think that we all, even with patent lacquer, are nothing more than insects of a moment on that ant-hill the earth, though we may be insects with stars and garters, places and offices!" -Ole the Tower Keeper.

Phil Plait reminds us of this humble truth: That life may be fragile and fleeting position in an eternal universe, but you certainly can't beat the view.

The Fruit Fly Debacle: The Scientists Speak

2008-10-26T15:03:00.002-04:00

Tip o' the nuerexin creating gene to A Blog Around the Clock.

Poli-Sci-Fi

2008-10-25T10:53:00.002-04:00

Sometimes, I wonder if the phrase "political science" is an oxymoron. I first saw this on MSNBC, but it's been commented on at Pharyngula and doubtless a few other science blogs:

Who in the science community hasn't heard of Drosophila? Hell, anyone who's taken biology in high school knows that they're popular genetic models for experimentation. Some very important research has come out of studying fruit flies, and for someone who has a son with a developmental disability, she should be the last person railing against fruit fly research.

Of course, the France angle was brought into it for kick. Well, according to Keith Olbermann, the research was being done in North Carolina. Of course France is a handy punching bag for her crowd, as evidenced by the White House cafeteria debacle.

We know how Palin feels about fruits anyway. In the interests of perserving scientific funding I propose that the common name of Drosophila be changed to Freedom Flies!

Economic Crisis for the Layperson

2008-09-21T17:12:00.003-04:00

Go directly to Calculated Risk, do not pass go, do not collect $200 without lending it to me first.

Seriously, it's the best up-to-date analysis I've seen lately.

Chemistry Myth: Glass Is A Liquid

2008-09-10T20:19:00.006-04:00

I've heard it before, and I keep coming across this idea: That glass is a liquid, it's just exceedingly slow-moving/viscous/lazy and unwilling to get off the couch. I don't blame people for believing it, I myself did for a long time. My science teacher told me this myth and I passed it on. It's just that there's something about glass, we take it for granted but whenever we actually start thinking about it, glass does seem like an amazing substance doesn't it? Granted it doesn't seem so amazing when you try walking straight into a glass door. So it seems credible that this incredibly smooth and ice-like substance might be some kind of exception to the rules of chemistry. Well I don't mean to shatter the mystery, but I promise to replace it with a much more interesting truth.

Glass, as you might already know is made from a mineral, silicon dioxide, which is the principal component of white sand. We heat the sand up, blow it into interesting shapes, and toss it into water to quench, or cool it rapidly (this is the key, as you will see in a minute.)

To explain glass, I need to explain the nature of liquid to solid transition. To do this, I'm going to show you a standard cooling curve for a container of water:

This curve looks similar for many substances, though some substances sublime under normal conditions, which means they turn directly from solid to gas and back. The reason I chose water here is because water is something we are all familiar with, and because I hope to get people to try experimenting at home. We all know water freezes at zero, but it won't go any lower until all of the water has turned to ice in a solution (we think of a mixture of water and ice as a solution in this example, even though they are the same compound.) However, you will notice a little dip in the curve that goes below zero, even though the water is still a liquid. This is liquid that is colder than the compound's melting point. A supercool liquid. How is this possible?

The answer lies in the simple fact that solids are solids because their molecules take on a rigid structure. Look at this rough representation of water sliding around in liquid form:

Now this diagram is somewhat problematic in many ways, but it will do for this explanation. Here we see our old friend the Mickey Mouse model of water. Now the reason hydrogen bonds to oxygen is that oxygen likes to donate an electron to hydrogen, and oxygen is more than happy to give one electron to each of two hydrogen (since hydrogen only has one positive charged proton to cancel out). This is how molecules try to equalize their charges. In nature, electromagnetic charges do their best to cancel each other out. However, oxygen is always hungry, it's so much more massive that hydrogen (about sixteen times as massive) and it has a slight negative charge even when its fully bonded to hydrogen. Hydrogen too, retains a slight positive charge.

Now in liquid water under normal conditions, these slight charges hold the water molecules together enough that most don't zing off into the air (cohesion). Though if you leave it lying around long enough it will evaporate, the water is warm enough that the molecules are bouncing around rather happily and don't stick in any rigid formation.

Now if you cool the water down slowly enough (and you may have had this experience with water, but it is common in alcoholic beverages.) the molecules will slow down very gradually, but they won't fall into any kind of order. They won't slide across each other as much, but they will kind of almost stand still in one place. This is the supercool liquid, there is no real structure to the molecules, they're not arranged in a way that would look like a solid. However, if you take this slowly cooled liquid (and once again, I encourage you to try this at home) and agitate it, it will freeze up and turn into ice almost instantaneously. This is because you have physically forced the molecules to turn, and they freeze up in an arranged structure, usually according to their partial charges, which looks a little like this:

As you can see, the slightly positively charged hydrogen ions are attracted to the slightly negatively charged oxygen ions. This is what a classic crystalline structure looks like.

"But Chemist," You ask, "What does this have to do with glass?"

Well, I'm glad you asked. Glass is like any other liquid when melted. As a mentioned before, it's silicon dioxide, which you may be familiar with in the form of sand, but also quartz. Yet you can't really see through most quartz crystals that well, they tend to let light in one way but not another. Glass doesn't have this problem. This is because unlike the ice in your refrigerator, when we freeze glass (that's the term we use for cooling anything into a solid) it's in an amorphous state, not crystalline. This means it's in that same disordered state I showed you when water is still liquid. This allows light to pass through it in all directions with minimal interference.

How do we get that to happen? It's the quenching process that I said was key earlier. While the glass is still in its plastic state having been melted, we rapidly cool it. This means that we get the temperature down low enough while its still a supercool liquid (which for glass is actually kind of hot) that it freezes instantaneously without rearranging its molecular structure much. Hence glass is not a liquid, it's a solid, albeit an amorphous solid. Its not super viscous, viscosity is a measure of how much molecules are attracted to each other in a liquid, the molecules in glass are locked in place, but they have no particular order.

The exact same thing can happen with water. Cool water rapidly enough and it will turn into amorphous ice, and will have similar glassy properties. However I don't recommend you try cooling water this rapidly at home. My guess is you would need a dangerously cold substance to cool water this rapidly, and I don't want anyone getting frostbite or worse. If you think you can pull it off with household materials you can try it (you might want to work with tiny amounts of water) just don't break out the liquid nitrogen, mmkay?

There you have it, a chemistry myth discredited. Questions? Comments?

Google Honors LHC

2008-09-10T11:01:00.003-04:00

One of the reasons I like Google is the sense I get that it has a certain respect for science. It's good to know technologists never forget their roots. Today, around 3:3oAM Eastern the LHC was go for proton injection. The protons didn't collide, they simply spun around in one direction as part of tests and the like before they start collecting data. I wonder if the Google logo getting pulled into the proton stream is a little reference to the people who say it will create a black hole.

Oh, and no, the LHC will not destroy the earth. Here is a website you can check to make sure it hasn't happened, and here's a website explaining why it won't happen. No need to worry about opening a gateway to hell. So here's to the LHC: May the data be good and error bars small.

Glenn T. Seaborg: Teacher

2008-09-09T21:26:00.006-04:00

Reading Glenn Seaborg's book, Adventure in the Atomic Age: From Watts to Washington, one is immediately captivated by the genial tone, the humble perspective, and the nuance of the writer. When I picked up the book I knew nothing about Seaborg, save a little of his work in nuclear chemistry, but when I set it down I could not help but feel I knew Glenn T. Seaborg on a much more personal level.

The autobiography starts with his beginnings as the child of immigrant parents from Sweden. He was born and spent the first part of his life in Ishpeming, Michigan. It is interesting to read about such things as the time the newly minted Green Bay Packers came to town. They would play the Ishpeming team, only to lose 33-0. His father was a skilled machinist, and he writes of the trouble he had finding employment and how the Great Depression affected his family. Foreshadowing later chapters, he informs us of how the Great Depression convinced him that government could be a force to help people.

One learns of how Seaborg would earn money for college, and his love of physical exercise as a cure-all. He attended the University of California Los Angelos shortly after it was founded, and testifies in the book to the ability of public universities to level the playing field by providing students like him with opportunities he would not have had otherwise.

He talks about walking into the President's office to ask for a graduate program to be instituted. Even today it would be unheard of for an undergraduate student to get a chance to talk to the people who ran the university. He would later find himself under the tutelage of one G.N. Lewis. Yes, that G.N. Lewis, the one that created the Lewis dot-diagram. He mentions how Lewis should have won the Nobel Prize, and likely would have if he had not alienated so many scientists with his take-no-prisoners attitude during colloquium.

It is interesting to note that he so often describes people in favorable terms whenever he found occasion to do so. He talks as fondly of the presidents during his tenure as AEC chairman, as they gave him cause to. He is the only person I have ever heard of to punch Reagan in the stomach and get away with it (though you'll have to read the book for that little story). Yet with all of the deserved praise he heaps on others, and even the acknowledgment of his own achievements, he remains rather modest. He talks about rubbing shoulders and butting heads with politicians as though these things were ordeals that he struggled with, yet we see from the results he achieved that he was an adept politician and diplomat himself.

He learned a great deal from watching people do their jobs successfully, and put these lessons to use in his own life. It is an inspirational work for it teaches you about the importance of working with people rather than against them. Even after other scientists shunned Edward Teller for his damaging testimony against J. Robert Oppenheimer during the Red Scare, Seaborg did not. Despite the fact that Seaborg recognized the manner in which Teller's vociferous anti-communism poisoned his thinking, he would do his best to work with him. Indeed, consensus building was his strong suit. While working for the AEC, even when he had the majority of commissioners on his side, he would work with the minority and negotiate until they could issue a unanimous opinion.

In the book, which was published in 2001, three years after his death in February in 1999, he takes on the role of prophet. He emphasizes the damaging effects of our dependence on fossil fuels, environmentally, politically, and pragmatically. He argues for the advent of safe and clean nuclear power with the frustrated patience of someone who knows he's being reasonable, if only people would listen. It is one thing to read a book where the author holds opinions similar to your own and to walk away agreeing with him or her. While not diametrically opposed to what Seaborg believed in, I did walk away with some of my misconceptions changed. While I've always been for nuclear power, my understanding of the risks involved with nuclear power was somewhat mistaken as I see now. I also understand the importance of a level of civility in public discourse, where before reading the book I had some very different ideas about it.

Seaborg was a true scientist, doing his best to make sure he remained productive after winning the Nobel Prize for his discovery of plutonium with Edwin McMillan (though Enrico Fermi and his team* was given premature credit for the discovery.) In many respects his creation of new elements made Seaborg into a 20th century alchemist, capable of transmuting one element into another. Yet when he was asked to head the AEC, he felt a duty to accept the position, so he did, and so it was for every position he held as something other than a scientist doing basic research.

Yet, he was also a teacher, and you get the sense that it was just as important to him as anything else. He wrote about sitting down to do all of the problems in the General Chemistry textbook before teaching the class after an extended period away from the academic world. When his secretary peeked in on him, his only comment was on how hard the questions were. This is made me smile. A lot of the book made me smile, and the last part of Glenn Seaborg's own writing, before it gives way to his son's epilogue, was A Letter To A Young Scientist. Being the person to whom the letter was addressed, I closed the book and waited until I could find more peaceful surroundings. When I finally got a chance to read it in peace, I appreciated the letter. It appropriately addressed my own specific fears and concerns, allaying them and encouraging me, and for that I am grateful.

*Added in light of a comment to this post.

Those Wacky Biologists

2008-09-03T11:47:00.004-04:00

Okay, I have no idea who came up with this, but it could easily have been the guys up in marketing, or the geeks down below.

Catchy though.

Yes, I need epMotion!

Tip o' the synthetic protein hat to Pharyngula.

Tuesday T-Shirt

2008-09-02T19:29:00.008-04:00

Almost Forgot!

Tip of the novelty hat to Psi*Psi for this one.

Considering my mishap in the lab today I felt this design was particularly appropriate:

Available at Yellow Ibis, ~~though they make it impossible to link to the specific shirt, so you'll have to find it yourself.~~ Now you can just click on the design above.

Thermite!

2008-08-31T19:53:00.002-04:00

You can never post too many thermite vids!