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]

Student Evaluations Don't Mean Much

Inside Higher Ed has just commented on a new study of student evaluations [New Questions on Student Evaluations]. The results are not surprising. They confirm all previous studies showing that student evaluations aren't what everyone thinks they are.

Previous studies suggested that students are rating generosity and personality and not quality of teaching. For example, a study of ratings on RateMyProfessor [‘Hotness’ and Quality] showed that,

... the hotter and easier professors are, the more likely they’ll get rated as a good teacher. As far as students — or whoever is rating professors on the open Rate My Professor site — are concerned, nothing predicts a quality instructor like hotness.

The new study from Ohio State University finds "... a strong correlation between grades in a course and reviews of professors, such that it is clear that students are rewarding those who reward them." Duh!

Now a cynic might say that this simply means that good teachers are doing such a good job that their students get higher grades. Thus, the evaluations truly represent the quality of the teacher and not how easy they mark. Well, that's not what the study suggests,

The Ohio State study, however, provides evidence for the more cynical/realistic interpretation — namely that professors who are easy (and aren’t necessarily the best teachers) earn good ratings. The way the Ohio State team did this was to look at grades in subsequent classes that would have relied on the learning in the class in which the students’ evaluations were studied. Their finding: no correlation between professor evaluations and the learning that is actually taking place.

The authors of the report show that student evaluations are practically worthless but in the interest of appeasing students they close with a mealy-mouthed sop as reported on the Inside Higher Ed site,

The authors stress that there are many ways — such as adjusting for student bias for easy graders or bias against certain groups of instructors — to continue to use student evaluations as one tool for measuring professors’ performance. But they write that, used alone and unadjusted, they appear highly questionable.

Let's see if I understand this logic .... student evaluations are biased and useless but instead of abolishing them we continue to use them to measure Professor's performance as long as we use other criteria as well.

Why? Why not get rid of student evaluations? We've known for decades that they don't work. Let's try and find another way for students and Professors to work together to improve university education. Student evaluations are ignored by all responsible Professors and they give students the false impression that their opinion is valued.

There has to be a better way. I believe that university students can provide useful and constructive criticism but only if they give up on the popularity contest and stop pretending that it has anything to do with quality of learning.

(As I write this, I'm supposed to be making up exam questions. I think I'll make some of them a bit easier .... )

[Hat Tip: Uncertain Principles]

Engineers Learn Workplace Skills

 
From the University of Toronto website comes this press release about how engineers learn workplace skills that will help them in their careers. The first two paragraphs are,

Gathered in the main dining room of the Faculty Club on the evening of Jan. 17, more than 100 engineering students sat down for an important professional lesson: dining etiquette. Led by Faculty Club manager Leanne Pepper, students were taken through the dos and don’ts of a five-course meal.

Organized by the Leaders of Tomorrow (LoT) program in chemical engineering and applied chemistry, the dining etiquette session was one of a series of talks and workshops that aim to develop the broader skills needed for engineers in the workplace.

Leanne is a friend of mine so I'll resist commenting.

Guernica

 
Remember Guernica? Thanks to the team of senior public health scientists and practitioners at Effect Measure for finding this video.

Is Nutritional Science Really a Science?

 
I have my doubts, and so does Jonah Lehrer [Why is Nutritional Science So Bad?].

John Kasich Interviews Atheist Brian Flemming about the Blasphemy Challenge

 
We don't get FOX News up here so I've never seen this John Kasich dude in action. Watch him interview Brian Flemming, the originator of the Blasphemy Challenge, at [onegood move]. With people like John Kasich around we have a long way to go before the majority gives up their supersitutions and becomes rational.

Kasich just doesn't get it. One is left with the distinct impression that Kasich has never, ever, questioned his religious beliefs. In other words, he has been so thoroughly brainwashed that alternative viewpoints just don't exist for him. Disgusting.

[Hat Tip: RichardDawkins.NET]

Monday's Molecular #11

 
Name this molecule. You must be specific. We need the correct common name.

This is another easy one for everyone who has ever taken biochemistry. This compound is one of the most important energy molecules in living cells. We will discuss the very important reactions that result in synthesis of this molecule after you've been given a chance to identify it.

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