Professors and Unions

 
I support unions so I don't have a problem with faculty unions and I don't have a problem with strikes if things can't be settled by negotiation.

Some people do have a problem with unions. They think that workers should always take what they're offered instead of disrupting the public by going on strike. Surprisingly, this neolithic attitude is common among students on university campuses—proving, once again, how different today's students are from those in the '60's.

The California Faculty Association may soon have to go on strike because the representatives of the schools refuse to make a decent offer after 20 months of negotiations. Faced with the possible disruption of classes, a student wrote this in a school newspaper,

If the teachers care more about getting paid rather than the education of the students, I say let them walk.

See how Janet Stemwedel of San Jose State University responds [I must have missed the line in my contract that said this is volunteer work].

Kid, if I only cared about getting paid, I'd be doing something else for a living.

Bravo Janet! Part of a good university education is learning how to see both sides of an issue. I hope your students benefit from your defense of a decent wage. Maybe they'll learn something from this experience.

Americans Never Landed on the Moon!

 
Friday's Urban Legend: FALSE

See Phil Plait (Bad Astronomy) on Bullshit! and learn about the moon landing hoax. Read about his experience with Penn & Teller [Penn & Teller, the Moon Hoax, and Me (Part I)]. Wait for Part 2.

A Simple Version of Photosynthesis

The 1988 Nobel Prize went to Johann Deisenhofer, Robert Huber, and Hartmut Michel for solving the structure of the first photosystem [see Nobel Laureates]. The photosystem was isolated from a purple bacterium and those bacteria have a relatively simple form of photosynthesis compared to cyanobacteria and chloroplasts.

It's worth looking at this simple version because it illustrates the main principles of photosynthesis without getting bogged down in excessive detail.

The type of photosystem is called photosystem II or PSII. Photons of light are absorbed by the chlorophyll molecules (P870) in this complex. Excited electrons are ejected from the chlorophyll molecules and they pass down a short path where they are picked up by quinone (Q). When Q acquires a pair of electrons, it brings in two protons from the cytoplasm (below) to form QH₂.


QH₂ diffuses in the membrane to another protein complex called the cytochrome bc₁ complex. This is the same complex that works in membrane associated electron transport, or respiration (as in mitochondria and non-photosynthetic bacteria: see Ubiquinone and the Proton Pump). The cytochrome bc₁ complex catalyzes the oxidation of QH₂ causing the release of protons on the outside of the membrane. The reaction—one of the most important reactions in biochemistry—is called the Q-cycle.

The net effect of these reactions is a light-driven proton pump that creates a gradient across the membrane. This is exactly what happens in respiration as well. The proton gradient, or protonmotive force, drives the synthesis of ATP by ATP synthase, another membrane protein.

The electrons that were ejected from the chlorophylls need to be replaced. The original electrons are passed on to cytochrome c by the cytochrome bc₁ complex during the Q-cycle reactions. Cytochrome c then diffuses back to the photosystem were it resupplies electrons to the chlorophylls in a cyclic pathway.

This is how light drives the synthesis of ATP.

Is Scot Adams an IDiot or does he just play one on TV?

 
Scot Adams, the creator of Dilbert, published an insane, unintelligible comment about the Big Bang and intelligent design. It looks for all the world like he's a tyical IDiot and PZ Myers shot him down [Will Scott Adams Never Learn?].

The Dilbert fans are up in arms. Some of them claim that we shouldn't take Scott Adams seriously—he was only joking. I don't think so. PZ was right. PZ has a history with this dingbat and he knows Adams isn't smart enough to be pulling our leg.

In any case, the question is now settled since Scott addresses it on his blog [Am I Serious?]. Here's his response,

I can’t rule out theory 1, that I am very, very, stupid and uninformed. That’s exactly the sort of thing that a person can’t know about himself. You really need to rely on other people for that diagnosis. Frankly, I’m rooting for that theory to be true; it would be comforting to be a member of the majority.

Then there’s the question of whether I believe what I say. This is a tricky question because people have wildly different opinions of what I’m actually saying. For example, do I believe in psychic powers, or did I simply write a story about a fascinating encounter with a self-described psychic in my book, The Dilbert Future? Interpretations vary.

I can only guess at my own motives for writing on these God-related topics. My understanding of the human mind is that our reasons are just rationalizations for our urges. I try to resist writing on these topics until the urge to do it pushes out all the other urges. I can’t explain the “why” of it. But I can tell you what I enjoy about it.

The part I like the most is the comments. I like the smart comments because they make me think. I like the dumb ones because they fascinate me and make me feel smart at the same time. I like the funny comments because they make me laugh. And the whole process makes me feel connected to something larger than myself.

Unlike most pundit-types, I don’t have a heavy investment in being right. I like to propose a line of reasoning and see what people think. If it exposes my ignorance – or more commonly, the reader misunderstands it and assumes ignorance, also known as the SHAAH method – that doesn’t bother me much.

Well, that does it for me. Scot Adams is an IDiot. What's more he seems to be the worst kind of IDiot, the kind that weaves and dodges in order to avoid being pinned down. Does he reject science in favor of GodDidIt? You bet he does, he's just too cowardly to come right out and admit it.

Critical Thinking in Medical Schools

 
Orac at Respectful Insolence wonders what's happening in medical schools. There's more and more of a tilt to "alternative medicine" (i.e., quackery) and this is disturbing. Read the latest at Critical thinking and the scientific method in medical education".

Another Canuck Blogger

 
There's a really good blog called Primordial Blog. As far as I can tell the author (Brian) lives in the Yukon—that's part of Canada (barely) so he must be Canadian.

Brian writes about Life at the Intersection of Science, Religion, Politics and Culture and he comes up with some really cool stuff. Check out the articles on global warming, floating windmills, and the evolution of whales.

Tangled Bank #72

 
Tangled Bank #72 has been posted at Ouroboros.

Buy a Conservative T-shirt

 
Here are three of my favorites. See the rest at ThoseShirts.com. Please tell me this is sarcasm.

Should Christians Be Armed?

 
While checking out Pat Boone's IDiotic statements about evolution [Charles Darwin's Funny Joke] I noticed this icon in the sidebar. Naturally I couldn't resist clicking on it.

I ended up at a site advertising the book Shooting Back. Here's what I read,

What would you do if armed terrorists broke into your church and starting attacking your friends with automatic weapons in the middle of a worship service?

Would you be prepared to defend yourself and other innocents?

Would you be justified in doing so?

Is it time for Americans to consider such once-unthinkable possibilities?

There is one man in the world who can address these questions with first-hand experience.

His name is Charl van Wyck – a South African who was faced with just such a shocking scenario.

In "Shooting Back: The Right and Duty of Self-Defense," van Wyk makes a biblical, Christian case for individuals arming themselves with guns, and does so more persuasively than perhaps any other author because he found himself in a church attacked by terrorists.

Wow! That's all we need. IDiots with guns. In church.

Don't you just love America?

Recognize This Guy?

 
Of course you do. That's PZ Myers of Pharyngula in a photo taken by a very talented photographer in someone's back yard in Oxford, UK.

PZ just got a nice write-up in the University of Minnesota at Morris News [PZ visits friend].

I get a mention too but no pictures of me.

Nobel Laureates: Deisenhofer, Huber, and Michel

 
The Nobel Prize in Chemistry 1988.

"for the determination of the three-dimensional structure of a photosynthetic reaction centre"

Johann Deisenhofer, Robert Huber, and Hartmut Michel received the Nobel Prize in 1988 for working out the structure of the first photosystem—the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis. We now know that this is a Photosystem II-type complex with a type II reaction center. Its chlorophyll molecules absorb a photon of light and catalyze the transfer of electrons from an electron donor (usually cytochrome c) to quinone.

The photosystem structure was one of the most complex structures ever solved by X-ray crystallography. Even today there are only a handful of solved structures that are as complicated as this one.

The complex is normally embedded in a lipid bilayer that surrounds the vertical α-helices shown in the figure. The large gray space-filling molecules in the middle are the chlorophyll molecules that absorb light. Excited electrons are released from the chlorophylls and transferred down toward the bottom of the molecule to reduce a bound quinone near the iron atom (brown dot).

The cytoplasm on the inside of the cell is at the bottom of this picture and the intermembrane space between the inner and outer bacterial membranes is at the top.

The reaction center chlorophylls need to be resupplied with electrons and these come from a type c-like cytochrome (purple) that's attached to the top of the photosystem. This particular cytochrome is unusual since it has multiple heme groups. In most other species the electron donor is cytochrome c.

As noted in the presentation speech, by solving the structure of a bacterial photosystem Deisenhofer, Huber, and Michel not only contributed to our understanding of photosynthesis but also to our understanding of all membrane proteins and of electron transfer reactions in general.

The structural determination awarded has led to a giant leap in our understanding of fundamental reactions in photosynthesis, the most important chemical reaction in the biosphere of our earth. But it has also consequences far outside the field of photosynthesis research. Not only photosynthesis and respiration are associated with membrane-bound proteins but also many other central biological functions, e. g. the transport of nutrients into cells, hormone action or nerve impulses. Proteins participating in these processes must span biological membranes, and the structure of the reaction center has delineated the structural principles for such proteins. Michel's methodological contribution has, in addition, the consequence that there is now hope that we can determine detailed structures also for many other membrane proteins. Not least important is the fact that the reaction center structure has given theoretical chemists an indispensable tool in their efforts to understand how biologic electron transfer over very large distances on a molecular scale can occur as rapidly as in one billionth (American English, trillionth) of a second. In a longer perspective it is possible that such research can lead to important energy technology in the form of artificial photosynthesis.

Poor IDiots, Wrong Again

 
GilDodgen over at Uncommon Descent has put his foot in it once again. This time the IDiots have jumped all over the book Chance & Necessity by Jacques Monod. The book was written 36 years ago but that doesn't seem to faze the IDiots. Anything that conflicts with their worldview is a target. See [Classic Darwinian Texts — (soon to be, if not already) On the Ash Heap of History].

Here's what GilDodgen has to say,

Read Monod’s book — a foundational Darwinian text. Nowhere in it does he ever address probabilistic resources; he just assumes on faith that random mutation and natural selection can produce everything.

Now I've seen some pretty stupid things over at the Dembski headquarters but calling Monod's book "a foundational Darwinian text" just about takes the cake. This is not classic Darwinism. Classic Darwinism tries to deny the role of chance as much as possible. What Monod does is emphasize the importance of chance and contingency.

The entire book is devoted to addressing the probability of evolution—something that seems to have escaped the notice of IDiots like GilDodgen. Here's a short excerpt from pages 43-44 where Monod explains his view of probability and the inability of natural selection to make predictions.

The thesis I shall present in this book is that the biosphere does not contain a predictable class of objects or of events but constitutes a particular occurrence, compatible indeed with first principles, but not deducible from those principles and therefore essentially unpredictable.

Let there be no misunderstanding here. In saying that as a class living beings are not predictable on the basis of first principles, I by no means intend to suggest that they are not explicable through these principles—that they transcend them in some way, and that other principles, applicable to living systems alone, must be invoked. .... All religions, nearly all philosophies, and even a part of science testify to the unwearying, heroic effort of mankind desperately denying its own contingency.

That ain't Darwinian, baby. Can you imagine Richard Dawkins ever saying that we are here by chance? And it sure as heck ain't intelligent design either—that's the part that annoys the IDiots.
The classic quote from Monod's book can be found on page 112. He discusses the various kinds of mutations that had been discovered by 1971. Then he concludes,

We call these events accidental; we say that they are random occurrences. And since they constitute the only possible source of modifications in the genetic text, itself the sole repository of the organism's hereditary structure, it necessarily follows that chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is ever likely to be revised.

You know what surprise me the most about the IDiots? It's not that they are ignorant about evolution, after all there are many scientists who cling to the old-fashioned Darwinian worldview as well. No, the thing that surprises me is that the IDiots are completely incapable of recognizing the different points of view within evolutionary biology. Here we have an example of an IDiot who has read Chance & Necessity but still calls it "a foundational Darwinian text." The mind boggles at such stupidity.

Memo to IDiots: there's more to evolution than Darwinism.

Of course GilDodgen can't resist taking a few other potshots at Monod. After all, Monod is French, an atheist, and (gasp!) a socialist to boot. Those evil socialist evolutionists, where do they get off caring for the downtrodden and the oppressed?

Footnote: GilDodgen begins his rant with,

I just pulled out my 1972 edition of Jacques Monod’s “classic” work, Chance and Necessity, subtitled A Philosophy for a Universe without Causality.

He can't even get the subtitle right. What he's quoting is a blurb on the cover that says "A philosophy for a universe without causality—by the Nobel Prize-winning French biologist." The actual subtitle is "An Essay on the Natural Philosophy of Modern Biology."

What Is a Valid Argument?

 
As part of the basic concept series, Janet Stemwedel explains arguments [Basic concepts: arguments]. For example, she says,

Here's an example of a valid argument:
1. Britney Spears is from Mars. (premise)
2. Martians have astounding vocal range and are great dancers. (premise)
3. Hence, Britney Spears has astounding vocal range and is a great dancer. (conclusion)

Are you convinced that this is a valid argument?

DNA Packaging and DNA Replication

 
The first part of this video shows how long strands of DNA are packaged in eukaryotic cells. It's pretty good. The second part is a demonstrating of how the replisome works. The replisome is a little molecular machine that copies DNA. The animation doesn't do a very good job of conveying the idea that the various components of the replisome interact with each other to form a compact blob at the replication fork.

The concept of a "molecular machine" was promoted by Bruce Alberts who worked on DNA replication. It gets the IDiots all in a tizzy whenever we talk about molecular machines. They think we're advocating intelligent design!



[Hat Tip: Living the Scientific Life]

A Typical Graduate Course in Biochemistry

 
Vince LiCata was kind enough to publish a generic course syllabus that applies to most graduate courses—and many senior undergraduate courses. Read it at MY NEW GRADUATE COURSE OFFERING.

[Hat Tip: The World's Fair]