Posted 9:21 AM by Paul

Flood the Zone
It's fun and easy. I did it. Follow the link...
Not Geniuses: "Flood the Zone" Friday is Here

Posted 9:49 AM by Paul

One more fair and balanced energy issue
It seems that the running meme in the business community (and the Bush admin.) is that no one has a financial incentive to maintain the power grid, so we need gov't cheese to help out these poor, financially incapable energy companies. Some may be quick to point to this as a "tragedy of the commons" scenario. I find that insane. It is not very smart business to build a billion dollar plant to produce energy, and then have no way to get that energy to market. It is also not very smart to run "last mile" lines into homes, and no supply lines. So, it seems to me, everyone has an interest in this. The problem (and it is, technically, the "tragedy of the commons", but sort of inverted) is that if you shirk your responsibility, your profit margin is bigger, and your competitor's margin (who had to make up for you) is smaller. All of this puts a perverse incentive on shirking.
Needless to say, the answer is not a gov't bailout (the ultimate perverse incentive!) but cooperative effort by energy suppliers and utilities to maintain and upgrade the grid, mandated if necessary by gov't. Of course, this has to be done in a fair and balanced manner.

Posted 9:12 AM by Paul

Some Fair and Balanced Questions
Fair and Balanced Question #1-Why does Texas have its own, independent energy grid?
Fair and Balanced Question #2-Why don't we know what caused yesterday's outage? Don't people work at these plants?
Fair and Balanced Question #3-Doesn't it seem like there is a better solution to grid overload than shutting down every plant in the network?

I report, you decide. (well, technically I don't report, and I can't force anyone to decide, but you get the point)

Posted 10:45 PM by Paul

What can I say? I saw a band wagon, I jumped on it-Go Al! Stick it to the Man! (Yada, Yada, Yada)

Posted 10:59 AM by Paul

An opening for Creationism?
Yesterday, I noticed this story from Kevin Drum about some changes in the wording of the chapter review topics in a (High School?) Biology textbook which, by some lights, open the door to discussion of religious Origins of Life ideas. Here is the relevant "review topic"

20. Finding and Communicating Information. Use the media center or Internet resources to study hypotheses for the origin of life that are alternatives to the hypotheses proposed by Oparin and Lerman. Analyze, review, and critique either Oparin’s or Lerman’s hypothesis as presented in your textbook along with one alternative hypothesis that you discover in your research.

Now, Oparin and Lerman have hypothetical timelines for the development of organisms from the primordial organic stew. Here are Oparin's and Lerman's ideas. Now, I have no real input on which is more likely, or whether there are other possible abiotogenic scenarios (my gut tells me that there are many rough paths toward life, given a fluid set of initial conditions, and no real constraints on wild-assed guessing). Now, the question is, are these changes really going to open up science classes to religious dogma?

My answer is a definite yes. In fact, I think that the new formulation opens a very profitable door to discussing the Creationist ideas. What, you say, not the answer you were expecting? Well, here's the rub. Any student who goes on the web looking for "Origins of Life" is bound to find 10 creationist sources for every scientific one (actually, a Google search shows that to be quite wrong, so consider my ass self-fact-checked), so a student might be likely to show up to class with a Creationist or ID theory (Intelligent Design). Now, it is staggeringly unlikely that the students have no idea of the Biblical Genesis story, so I don't think the idea will be new to them. But is any of this relevant to a science class, you might ask? After all, this seems like it belongs in a social studies or religion class...

NO! In fact, this discussion belongs right in the middle of a science class. A student of science must understand what it means to ask and answer a question using logic, reason, and the experimental method. Further, they must understand that when someone presents an explanation for events, it may come in many forms only some of which are scientific If a theory or hypothesis is subject to experimental verification, it is scientific. If it is not, then it is not science.

Aha, you might say, this makes the other origins of life and evolution arguments unscientific, right? After all, we can't go back in time and watch the primordial slime turn into people, right?

Well, that's true, but misleading. While we can't turn back the clock, we can do experiments to test predictions here and now made by Abiotic origins theories and by Evolutionary theory (the Miller/Urey experiment is a classic example). On the other hand, any notion that a Divine intervention (or Prime Mover, if you like the cold, pseudoscientific language approach) was necessary to start life is by definition untestable.

So, it seems to me that, perversely, this effort presumably by Creationists to inject their ideas into the classroom provides a terrific opportunity to educate students on why those ideas are not science. As a student of the sciences, and a partisan of freedom of thought and speech, I don't find it a good idea to suppress the Creationist ideas-it is a much better to combat them openly and honestly, and explain why they don't fit into a scientific rubric.

It seems to me that the best outcome of this question being posed to a class is that most of the students will come up with various hypotheses that include no mention of Deities intervening, but some student or students will include Creationist or ID hypotheses. A good science teacher can use this to contrast a viable, testable scientific hypothesis with one that is not. If the students are told they are not allowed to mention or discuss Creationism, it makes it seem that we are trying to suppress the information, which in the time honored tradition of teenagers everywhere, will make them seek it out. Of course, the teacher might fail to demonstrate how Creationism is unscientific, but in that case, you have a bad teacher, not a bad policy or a bad question, which is a whole separate issue.

Posted 2:41 PM by Paul

Update to the Climate Change post- In the comments, "Charles Dodgson" points out my inability to understand common notation. Here is a link to the original source of the Climate Change stories (Charlie's Diary)

Posted 11:30 AM by Paul

Global Climate Change Redux
Interesting pointers from Charles Dodgson to some stories about the very odd weather conditions in several parts of the world right now, including ridiculous heat in Europe, and very cold water off the Eastern Seaboard. He also includes a link to an article at Woods Hole Oceanographic Institute about the role of ocean currents in abrupt climate change.
Now, I am certainly no expert in climate change, but one of the major things that critics of the Climate Change science point out is that there are many apparently conflicting predictions out there, including predictions of substantial warming as well as predictions of a new Ice Age (that is the link). Now, I think the criticism tends to be over the top (Andrew Northup points this out, and is much funnier than me), but it seems that a great deal of the problem stems from basic misunderstanding of the question.

It is, by any measure, a tremendously difficult thing to predict what the global climate will be like at any point in the future. Many very smart people use very complicated models to predict very general things, but that is about it. However, much of the seeming conflict comes from increased understanding of the system. Let me see if I can give an example.

A good example that is readily accessible to me might be the historical use of antibiotics. It is clear that since the introduction of antibiotics in the first half of the 20th century (counting early Sulfa drugs), they have been a tremendous boon, extending lifespans, and, coupled with childhood vaccinations, making infectious disease a significantly smaller threat in developed countries. However, the way they are used has changed a great deal. While doctors still prescribe antibiotics frequently to children, this practice is being actively discouraged by experts in the field, and attempts to curb overuse of antibiotics in animal feed are being made (I believe it has been banned in Europe and Canada, and may soon be in the US). Now, the effects of antibiotics have not changed-giving constant low doses to livestock still makes them grow larger faster, but the overall effect on human health is now better understood.

Simply put, using antibiotics in feed, and overuse of antibiotics in medicine, particularly pediatrics, has lead to substantial resistance to antibiotics in many microbes, and resurgent bacterial infections as causes of death. Gram negative and particularly gram-positive sepsis has become a very large problem, particularly in patients undergoing surgical procedures. These infections tend to be difficult to treat because they can be overwhelming to the system, and antibiotics often fail to work because bacteria in hospitals are so often resistant to antibiotics.

All of this may seem to you to have nothing to do with Global Warming, but the reality is that our perspective on Climate Change is similar to that of microbiologists and doctors in the 1950's. We know that industrial production has short and long term economic benefits, and we suspect that there are high long term costs, but we don't know how they will turn out.

Now, of course it would have been ludicrous to suggest denying people lifesaving medicines then (or now) in the name of preventing the development of antibiotic resistance. However, prohibiting use in livestock might have been very helpful, if anyone had been farsighted enough to do that. Likewise, stressing development of rapid diagnostics rather than knee-jerk prophylactic use of antibiotics might have prolonged the useful life of early antibiotics, and stemmed the crisis. Likewise, taking action now to stem human perturbation of the global climate might cost a lot less, in the long run, than dealing with the consequences later, what ever they might turn out to be.

Posted 11:24 AM by Paul

Learn your history!
Reading these letters to the editor wrt Condi Rice's comparison of Iraq to post-WWII German occupation, I couldn't help notice the distinct lack of historical knowledge in the second (the first is a fine, first person account of the occupation of Germany)[Iraq Is Not Post-WWII Germany]. Now, the second letter, in full (it is too short to excerpt).

No! Postwar Iraq is not analogous to postwar Germany.

Germany had a homogenous society that had a substantially democratic form of government (before Hitler). Iraq didn't exist until the British drew arbitrary lines in the sand to create it, without regard for the disparate, distinct tribes whose history — and legacy — is tribal wars and, often, a nomadic, theocratic culture.

The absence of this fundamental understanding of the people and history of the region has led this administration on a path of destruction and self-destruction. President Bush and company need to read a few history books.

Now, I happen to agree with his point, and I certainly acknowledge that Iraq's borders, drawn by the British as part of an attempt to create balanced powers in the region, without regard to internal tensions, create a large measure of the problems (ahem, oil, Israel). BUT, how can anyone argue that Germany had a "substantially democratic" form of government. Yes, of course, the Weimar Republic was a democracy of sorts, and this statement is literally accurate, but it misses the point entirely. One of the major forces leading to the rise of Hitler in Germany was a nation unused to the form and function of democracy.
It is helpful to recall that the nation of Germany was very young in 1933, having been officially formed in, IIRC, 1877, basically by the force of the strong Prussian kingdom assimilating the other Germanic central European states of the former Holy Roman Empire. This basically Prussian state was ruled by autocrats, such as Otto von Bismarck and Kaiser Wilhelm, until WWI. After the war, the Western Powers (Britain and France, principally) forced an arduous and destabilizing peace on the Central Powers (Germany and Austria-Hungary, but principally Germany). This peace included the dissolution of the Kaiser's government and the establishment of the Weimar Republic. So, when Hitler came to power in 1933, democracy had "flourished" in Germany for all of 14 years. Additionally, the Weimar Republic was not nearly as homogenous as Mr. Yablow is suggesting. Political and social factions in Germany made for substantial potential for internal strife. It was largely economic impoverishment, lost national pride, and factional politics that allowed for the rise of fascism in Germany (and Italy, for that matter)
As I said, I agree with Mr. Yablow's point, but the main reasons post-WWII Germany is different are money and troops.
In the words of Mr. Yablow's letter, he needs to read a few (more)history books.

Posted 9:43 AM by Paul

Happy Birthday to Me
They say its your birthday, well its my birthday too, yeah!
The big 3-0, I made it...

Posted 5:59 PM by Paul

Recall follies to include Kindergarten Cop
According to several reliable sources relayed by the anonymousMan Without Qualities, Ahhnold is running for Governor of CA, which means Dick Riordan isn't. Should be very interesting...

Posted 5:45 PM by Paul

Here is a very nice (long) post by Dwight Meredith about campaign promises, and about the stark way in which Dubya has broken his promise to be "a uniter, not a divider". As written at Seeing The Forest many times, watch what they do, not what they say...

Posted 5:12 PM by Paul

The Grad School Blues
A post by Derek Lowe and a follow-up by Chad Orzel about "Stockholm Syndrome", or "Why I won't do the experiment that will get me my Ph.D." struck a cord with me, not surprisingly. As both of them noted, Grad School can become a very comfortable place to be. Sure, the money is bad, but hey, if they aren't paying much, you don't have to work hard, right? Additionally, as they both noted, as you go through grad school, you go from neophyte to resident expert in a couple of years. After grade school, high school, and college, you are certain that you have to go right back to the beginning when you leave (you're right, too!), so what's the hurry? Plus, if you go academic, the money doesn't exactly get a lot better real fast.
So, what is a grad student to do? Well, my experience mirrors others, I am sure, but eventually life catches up to you, and you realize it is time to get on with it. Either that, or you begin to hate your labmates so much that you can barely stand to look at them, and you realize that it is graduate or go to prison for aggravated mayhem, so graduate it is! Finally, working on the minutiae of a single project can get excruciatingly boring after a while, which also helps.
So, what is my advice to grad students out there? I don't know (run like hell?). But basically, think of grad school as a time for learning lots of new things, and living on tight budgets. There may be lots of stress (or not), there may be lots of fun too. But in the end, you learn mostly about how to motivate yourself when no one else will, and that is the most valuable lesson. I think students should make sure to have fun in grad school-go to the seminars, make friends, learn as much as you can, because once you leave, the pressure ratchets up, and all of those things go out the window (especially if you have a family).

Posted 3:07 PM by Paul

An Evolution Argument

Back to the science type content, at least temporarily. I have repeatedly outlined arguments for Evolution v. Creationism here, but there is one strong argument that I have overlooked, or rather, not espoused. It is not an argument against Creationism per se, but it is a core argument of microbiology, and also of ecology, that is best explained by the Theory of Natural Selection. Of course, a Creationist "just so" story would also suffice, but would run afoul of Ockham's Razor, as usual. Nevertheless, here it is (note: this post is inspired in part by my current reading, The Future of Life, by eminent naturalist and entomologist E.O. Wilson);
It is a truism in microbiology that bacteria will live in the presence of carbon, phosphorus, nitrogen, sulfur and energy (which might come from light or from chemical sources, including organic and inorganic chemicals). It used to be thought that the Sun was the source of all biospheric energy, but the discovery of autolithotrophic bacteria (literally, bacteria that eat rock) put the lie to that. The truism goes even deeper than what is noted above, however; There is no sterile environment on Earth. Now of course, you can take a place, say the inside of an autoclave, and make it sterile, but there is simply no place on Earth that is naturally free of microbial life. To put it bluntly, microbes are the world's experts at extracting life from inorganic matter.
So why is this an argument for Evolution? Well, from my viewpoint, there are two possibilities-one is a Creationist "just so" story. God, in his or her wisdom, created that Universe, and filled it with life, squeezing a bacterium into absolutely every single conceivable niche. Alternatively, 4 billion years ago, the Earth coalesced from the swirl of hot gas and dust that was the Solar System, and a geologic blink later, microbes began to form to utilize the energies of the world around them. As they multiplied, they filled the abiotic world and started using the resources, along the way creating new environments and niches. At this point, I am telling an Evolutionary "just so" story (if we ignore the fossil record and molecular phylogeny data). However, a theory of Natural Selection suggests that living organisms will fill every available niche, i.e. will compete and adapt to utilize resources maximally. So Evolution makes a prediction-for every potential energy and nutrient source you will find an organism that uses it. This prediction can (and has) been tested. It has held up so well, that microbiologists don't even consider it a question anymore. It is so routine that a course can be (and often is) built with the following structure; 1)find a chemical, either naturally occuring or synthetic and 2) take a soil or water sample and add that chemical to it, 3) incubate for a couple of weeks at 30 or 37 deg. C, wait for bacteria that can use the chemical to grow. This virtually always works. Essentially, what you are doing is adding an energetic or chemical input to a very competitive system that is in equilibrium. When you add the new input, whatever organism can use it best will grow, until a new equilibrium is reached. As my recent boss wrote (to paraphrase) "With bacteria, you get what you ask for".
Unfortunately, I don't think that this argument works well for people who are not well versed in biology or microbiology. But it is a hugely useful thing to remember when thinking about life and ecosystems-nothing is wasted.