NCBI ROFL and the climate email "controversy"

This title says it all to someone who has no idea what either acronym means in the same way that the statements "I've just completed Mike's Nature trick . . . to hide the decline," and "We can't account for the lack of warming at them moment and it is a travesty that we can't" are self-explanatory to someone who doesn't understand that a fair proportion of the words in those sentences have technical meanings which differ substantially from their common meanings. That is, if the acronyms NCBI ROFL mean anything to you, you are likely to be an internet junkie and a scientist. Below is a reasonably informative video explaining what I'm talking about.

But first, before we get distracted and annoyed, NCBI ROFL is fantastic and hilarious. I wish I knew which grad students are behind it.

On student fees at the University of California

UC tuition has gone up infinity percent since the early 80s, so clearly the ASUC's current ways of advocating for students in what is by far the most important arena are made of fail. So here's my plan for the ASUC re: dealing with superhuge tuition increases. Instead of waiting to be taken advantage of because we are the least effective group at advocating for ourselves--that is, our union sucks the most--we should get preemptive.

The ASUC should behave like a real union for grownups for once by getting the University of California to sign a legal agreement prohibiting them from raising student fees by more than a set amount each semester. A cap of a 5% increase per semester, roughly three times the annual inflation rate, seems like a reasonable figure to shoot for.

Naturally, the University probably isn't going to want to sign such a document. If the University refuses to sign, this would give the students the opportunity to engage in a meaningful, directly effective protest without feeling like impotent little children throwing a hissy fit because mommy broke her promise to get ice cream (at least this is how I felt during the recent protests).

Also, a note to the planners of those recent protests: it's really dumb organizational strategy to specify a bunch of reasons for protesting with which many of your diverse group of potential co-protesters may not agree. Keep it broad and simple, not detailed and therefore potentially alienating. In particular, a lot of the protest fliers suggested that the Regents spend the endowment. I believe this suggestion to be monumentally stupid and ill-informed, and it detracted from my feelings of solidarity with the protest. Of course, the fact that I believe the protest was directed primarily at the wrong group of people--the Regents rather than Sacramento, Washington, and to a minor degree, the ASUC--also detracted from my enthusiasm for this particular protest despite my deep dissatisfaction with the situation.

Excellent bit of dietary research skepticism

I've long been skeptical of the scientific validity of nearly all dietary research. I simply don't believe that the experimental design, controls, and logic standard in the discipline are sufficiently rigorous to earn the results the honor of being considered scientific.

Now, I don't blame the researchers to a very great degree. Even their unobjectionable results are often made objectionable by sensationalistic media, oversimplification, and popular incomprehension. Also, considering that the academics of every discipline are expected to conform their research to the standards of their discipline, I am inclined less to blame the individual researchers than to blame the established standards of the field as a whole.

That said, dietary research sucks. Its poor standards compromise public understanding of and appreciation for science. It uses the good name of science to influence laymen to believe entirely in "facts"--often "facts" with little relation to facts--in which laypeople probably wouldn't believe otherwise. It tells unintentional untruths, and even outright lies, with unacceptable regularity.

Now that I'm done ranting, you can read this excellent attempt to set the facts straight.

Someone on the internet is WRONG!!

A while ago, people were making a fairly big deal about potential problems with the distinguishing feature of wikipedia: namely, that anyone can edit it. Though these criticisms were valid, I feel they were somewhat overblown. A discriminating reader knows enough to disbelieve information entered by vandals and the overly opinionated, and these biased/jocose authors aren't likely to frequent the more obscure pages which actually convey information of which readers are entirely unaware.

I feel that the problem epitomized by The Huffington Post heath/science section is much more threatening. On the internet, a large, influential publication may be disproportionately influenced by one [in this case, one very credulous] individual in a way which is not possible in traditional media. Due to Arianna Huffington's beliefs in supremely questionable science and medicine, The Huffington Post's health/science section is a collection of crackpottery, unverified claims, and outright lies. Despite its occasionally disgraceful quality, The Huffington Post is one of the internet's most powerful sites, drawing and doubtless informing and influencing thousands (millions?) of readers per day. This is a much bigger problem than the vague possibility that some credulous individual might pick up an isolated untruth on a wikipedia page, for meanwhile that same credulous individual is swimming in an entire ocean of bullshit at The Huffington Post.

Not only have they identified Copernicus' remains,

they've confirmed the longstanding rumor that he was a blue-eyed charmer.

Required reading

Eloquent, thoughtful, and heartfelt condemnation of mathematics education: Lockhart's Lament [pdf].

Why does your average snake oil salesman have a larger audience than your average scientist?

Degree of certainty.

My simple yet reasonably accurate height predictor

A child's height above the average is likely to be the average of the differences between his parents' height and the average height for their respective genders.

For example, call the average height for men 5'10" and the average height for women 5'4". My dad's height is 6'2" and my mom's height is 5'8", so my height is predicted to be [(6'2"-5'10") + (5'8"-5'4")] / 2 = 4", so my height is predicted to be 6'2", one inch off my actual height of 6'3".

And yes, I have tested the equation for people other than me.

Abberant filmmaking processes

I want to see documentaries elaborating on the production of these films.

The making of one involved precarious rafting through the Amazon, murder-suicide threats, theft of camera and monkeys, standard use of violent arguments as a performance preparation technique, and a lead actor who had been recently diagnosed with schizophrenia: Aguirre, the Wrath of God.

The second was made by Kim Jong Il with the help of his secret police, who kidnapped the director and lead actress and then forced them to make the film: Pulgasari.

Note that the former is considered one of the best independent, low-budget films ever made, whereas the latter is considered amusingly atrocious.

"...and the next sentence of the proof begins with the most frightening word in mathematics: 'clearly'..."

In meso

Hokay, so by conventional means, the success rate for crystallizing membrane proteins is only marginally better than the success rate for getting Congress to pass legislation requiring them to know what they're talking about. Some of the reasons for this are fairly simple. Firstly, membrane proteins are, believe it or not, components of the cellular membrane, so they are "engineered" to be well-formed iff they are embedded in a membrane-like structure. Aqueous solutions, the traditional standard for crystallography and for most other things, are not chemically similar to membranes. Therefore, just getting membrane proteins to fold homogeneously in a standard crystallographic screen is difficult. Secondly--this is probably not a difficulty significantly addressed by the paper that is the reason for this entry--most membrane proteins have intrinsically disordered ("floppy loop") regions which protrude from the membrane. Obviously, the degree of the protein's floppiness is inversely proportional to the likelihood of of its forming a homogeneous three dimensional structure. One technique to combat this issue that has been used with a fair degree of success is to engineer artificial proteins with the "floppy bits" removed. Of course, there are major problems with this strategy that I'll let you figure out on your own.

This new crystallization strategy combats the first problem with a fair degree of success. This is big news, trust me.

Any exceptions in the audience?

Mad scientist?

Interesting read

Fascinating article speculating in detail (read: at length) on the effects of Ted Kaczynski's subjection at Harvard to mild torture by the CIA's MKULTRA program and the university's ill-conceived general education requirement.

Excellent post containing a semi-trivial fact I've long been vaguely curious about

"I noted that the concentration of water in water (about as high as a real concentration can be) is 55 M..."

As good a definition as any

"A person is not old until regrets take the place of hopes and plans."
-Scott Nearing

If you think about them as means rather than ends in themselves, they really are spectacularly useless.

“Humans are incapable of securely storing high-quality cryptographic keys, and they have unacceptable speed and accuracy when performing cryptographic operations. (They are also large, expensive to maintain, difficult to manage, and they pollute the environment. It is astonishing that these devices continue to be manufactured and deployed. But they are sufficiently pervasive that we must design our protocols around their limitations.)”
— Kaufman, Perlman, and Speciner

A paradoxotaur ate my homework.

Jokes.com

Demetri Martin - Mytho-Zoology

Joke of the Day
Stand-Up Comedy

Free Online Games
More Funny Videos

Modern biology isn't particularly Darwinian.

It continually strikes me that, in their willfully ignorant screeds, the opponents of evolution prefer to invoke the name of Darwin rather than call the field by its modern name: evolutionary biology. Perhaps this is a conscious choice to make evolutionary biology seem more antiquated and hidebound than it is, or perhaps these people simply fail to understand that calling the evolving field of evolutionary biology "Darwinism" is about as accurate and current as calling modern quantum chromodynamics "Newtonianism."

Many non-scientists and even some novice scientists have a fundamental misunderstanding about the process of science. More specifically, they fail to understand what makes a discovery great, or at least good enough to merit passionate discussion for the next several hundred years.

When I was taking high school physics, a classmate informed me that Niels Bohr wasn't a very great scientist because most of his theories were wrong. Anyone who knows me well knows that there are few better ways to get my goat than by dissing Niels Bohr, but it took me a good number of years to realize just how wrong my classmate's theory of scientific worth was (and probably still is).

My classmate wasn't mistaken as to the limitations of Bohr's theories; his 1913 model of the atom, for instance, fails in ways both subtle (no, orbitals can't really be visualized) and obvious (it can't explain the Zeeman effect or the behavior of atoms with more than one electron). My classmate's mistake was his incorrect valuation of scientific worth. In science, a concept is valued not for being absolutely correct, but for being both germane and germinant. Germane: does the concept reflect the available data? Does it say something interesting and meaningful? Germinant: how powerfully does the concept motivate the growth and formation of new concepts?

Clearly, by these standards, Bohr's 1913 model was of the highest scientific worth, for it was both germane--it explained the available data far more completely than any preceding model--and germinant--I don't think even my classmate would attempt to dispute this qualification. The model's absolute Correctness has little relevance when evaluating its scientific value.

To return to my original point, biologists revere Darwin's work not because it is correct, but because it has great scientific worth by my standards; it was extremely germane at the time of its publication, and it continues to be beautifully germinant. Scientists' respect for Darwin is predicated more on the doors of inquiry he is perceived to have opened rather than the explicit content of his publications. Darwin's work has its evidenciary and deductive limitations. Modern biology retains only the barest kernel of Darwin's general thesis. It owes a great debt to Darwin, but it is "Darwinian" in only the very loosest sense. Thinking of evolutionary biology as "Darwinism" both inhibits your understanding of it, and perhaps even betrays insufficient understanding of science as a whole.

Incidentally: 7 Major "Missing Links" Since Darwin.

Sigh... to think we are still devoting a lot of resources to this, and the more ignorant environmentalists still support it

Yes, it's again time for the me to rant about biofuels. Note that the neologism "biofuels" implies that said fuels are derived from biological sources, but not necessarily that they are biologically friendly.

"For each billion ethanol-equivalent gallons of fuel produced and combusted in the US, the combined climate-change and health costs are $469 million for gasoline, $472–952 million for corn ethanol depending on biorefinery heat source (natural gas, corn stover, or coal) and technology, but only $123–208 million for cellulosic ethanol depending on feedstock (prairie biomass, Miscanthus, corn stover, or switchgrass)."

In practice, the costs of corn ethanol are much closer to the upper bound of $952 million than they are to the lower bound of $472 million, because the very real corn ethanol currently produced in huge quantities thanks to massive Federal support is grown and refined using mostly coal power.

Therefore, if I were going to reduce this paper to an oversimplified soundbite, much as mainstream media might if they were covering this topic, I'd say: CORN ETHANOL IS TWICE AS BAD FOR THE ENVIRONMENT AS GASOLINE.

Save us, Steven Chu!

Let's see if you are as smart as I am (without even taking an undoubtedly reliable online IQ test!)

I knew with absolute certainty which Senator the following headline is referring to without opening the link:
"Senator calls for 'truth commission' on Bush administration"

How do you get to be smart? Never stop asking "why."

"A DIALOGUE WITH SARAH, AGED 3: IN WHICH IT IS SHOWN THAT IF YOUR DAD IS A CHEMISTRY PROFESSOR, ASKING “WHY” CAN BE DANGEROUS"

Food.

As a person in the habit of eating semi-regularly, I am interested in food. Therefore, I found this article illuminating and insightful.

Openness and freedom of information exchange is vital to science and to the world in general

Free the facts!

Please, consider publishing on arXiv, PLoS, or other open-access publication.

Outstanding review of dark matter

I'm not sufficiently expert in astrophysics to assess the accuracy of this review, but I found it extremely informative and interesting.

Two highlights of my archived links

Nerd Self-Help (insightful and hilarious)
"26 GHz isn’t bad for the new kid on the block:" the [quite near] future of computing?

Hmm

Is this past entry prophetic?

In which Ann Landers is unintentionally meta

"Vow not to make a promise you don't think you can keep."
-Ann Landers

Molecular mechanism for the umami taste synergism

As far as I understand it, umami is the uniquely delicious glutinous taste nicely exploited by many Asian foods. There isn't an English word for the concept (unless "umami" is borrowed from the Japanese as it is here).

You know that metallic smell?

That smell you probably associate with most metals is only indirectly metallic. What you're actually smelling is the organic compound 1-octen-3-one, formed by the redox reaction between the metal and you.

An unusually clearheaded way to think about decision making from a many-worlds perspective

"What I do want for myself, is for the largest possible proportion of my future selves to lead eudaimonic existences, that is, to be happy."
-Eliezer Yudowsky

And remember that due to the cumulative nature of science, each wasted minute slows progress not linearly, but exponentially

"Science magazine reports a surprising and important scientific development that has been years in the making: US research faculty now spend an estimated 42% of what they consider “research time” on on pre- and post-award administrative activities — on writing progress reports, satisfying intricate rules for revenue management, working on review boards, and so on."

Favorite paper read today

Memory Traces in Dynamical Systems

I like papers that [at least try to] establish limits on things.

This discovery is about as distant from my field of research as you can get, but I find it very exciting

"This could be the first magma observatory in the Earth," Marsh said. "This is a singular event of first contact with inner Earth, where magma lives."

Whenever I read something unexpected in the AP, I always get an extra little shock because it's the AP

"Karzai said his country doesn't want to depend on international handouts forever, but stressed the help will still be needed for some time — not before 'we have taken from President Bush and the next administration billions and billions more dollars,' he joked."

Right... joked... ha ha ha

My confidence over time that the bailout is in the best interest of the economy

Steven Chu, Secretary of Energy

I'm very happy with the reports of Obama's decision to nominate Steven Chu Secretary of Energy. Though I think Obama is quite open to finding alternative sources of energy, I think it is an area he knows very little about, as evidenced by nearly everything I have ever heard him say on the topic. Therefore, the nomination of such a successful, formidible intellectual as Chu as Obama's chief energy advisor should have the most salutary effects on Federal energy policy in coming years.

Education: cutting off the long tails to push the mean in the right direction

I'm not at all in love with this article, but I do think the general idea is quite valid. Since students generally change teachers every year and students take annual standardized tests, we can use testing data to get a very rough idea of how their teachers compare. As Gladwell puts it:

Suppose that Mrs. Brown and Mr. Smith both teach a classroom of third graders who score at the fiftieth percentile on math and reading tests on the first day of school, in September. When the students are retested, in June, Mrs. Brown’s class scores at the seventieth percentile, while Mr. Smith’s students have fallen to the fortieth percentile. That change in the students’ rankings, value-added theory says, is a meaningful indicator of how much more effective Mrs. Brown is as a teacher than Mr. Smith.

No one could reasonably expect this model to distinguish between two teachers of reasonably comparable skill. However, I think it would be reasonable to use these change in test score values to identify blatantly subpar teachers, and then remove them from the educational system. For example, though this numerical system is very crude, and though I entirely dislike its reliance upon standardized tests, I think you wouldn't go far wrong if you were to fire the teachers whom this "value-added" model identifies as being in the bottom 5%. The model is so crude that many of the fired teachers would not actually be among the worst 5% or even 10% of teachers, but I would be shocked if a non-negligible number of them weren't in the bottom 50%. And eliminating any subaverage element from the educational system is surely a means of pushing it in the right direction.

Having been a sometimes disaffected participant in the US educational system for approximately the last two decades, I naturally have a lot of ideas for the modification and improvement of education, and perhaps I'll continue to expand on them in future entries.

The 21st century version of book burning

"They don't need to burn the books, they just remove them." The UK Home Office is completely eliminating access to all websites that fall under their extremely broad definition of "child pornography" for everyone in the UK. Wellington Grey's fairly incisive take on the topic. Any errors in this entry are the result of its being written while my cockatiel nibbles on the keys.

Philosophies of bartending

I hear there's going to be a rumble between the neo-classicists and the revivalists under the bridge at midnight. Be there. You may, however, want to avoid the candied bacon martinis.

The impatient internet user's fallacy

The frequency with which one refreshes a web page is NOT directly proportional to the frequency at which the page updates.

On the dangers of thinking you know more than you do

My understanding of the ongoing financial crisis: for the past few decades, the financial sector has been a place in the economy where a lot of mediocre, not particularly smart people who are willing to totally buy into their own corporate mythology can find their niche and feel very smart and important. And the current financial crisis is the inevitable result of this state of affairs. Putting mediocre, incurious people with a tenuous grip on reality in positions of power seldom turns out well.

Interest in pseudomedicine is declining

(at least among the internet literate).

A kind of Sokal affair with a 200-year time delay?

I'm not sure if the joke is on the author of the satire or on the historians.

Obama's intellectualism probably made him even more unelectable than his race

"Barack Obama’s election is a milestone in more than his pigmentation. The second most remarkable thing about his election is that American voters have just picked a president who is an open, out-of-the-closet, practicing intellectual."

Two scientist quotes for today, stolen from others' blogs

"My group theory teacher, Prof. Daniel Freedman, had some interesting professorial habits. When invoking some bit of background knowledge with which we were all supposed to have been familiar, he would say, As you learned in high school. . .' Typically, this would make a lecture sound a bit like the following:
'To finish the proof, note that we're taking the trace of a product of matrices. As you learned in high school, the trace is invariant under cyclic permutations. . .'"

"'One day sir, you may tax it.'
-Michael Faraday, asked by the British Minister of Finance about the practical value of electricity"

A long stay in Sweden is looking better than ever

I'm guessing that the US isn't planning on matching this move.

Great reading

I just discovered an absolutely delightful book. Scientific Laws, Principles, and Theories by Robert Krebs lists the major contributions to science over the past thousand years or so alphabetically by the name of the scientists involved. Great reading, suitable for everyone from motivated middle schoolers to adults.

How to express this symbolically?

"Opposite and similar are opposites."
-D. Hofstadter

A major issue in Iran: pesky spying animals

Iran has captured and detained both spying squirrels and, more recently, perfidious spy pigeons.

On the $700bil figure in the bailout plan:

"'It's not based on any particular data point,' a Treasury spokeswoman told Forbes.com Tuesday. 'We just wanted to choose a really large number.'"