Complementary and Alternative Medicine Exposed

 
Skeptics Canada is launching a year-long campaign against complementary and alternative medicine (CAM). The opening salvo will be fired tonight at the monthly meeting. Go to the Ontario Institute for Studies in Education (OISE) Building on Bloor St., just west of the St. George subway stop. The meeting is in rm 2211 from 7-9 pm.

First in a series of presentations on the topic of complementary and alternative medicine. Professor Michael De Robertis will speak on homeopathy, and award-winning journalists Paul Benedetti and Wayne MacPhail will speak on chiropractic. As well, a public test of one or more alt-med treatments is being planned.

Unfortunately, I won't be able to make it because of another commitment but I can assure you that it will be very entertaining. This is a good cause. Alternative medicine is gaining in popularity as more and more people strart looking for simple cures. Don't forget why it's called "alternative" medicine—it's because it's the alternative to rational evidence-based medicine.

The latest version of Skeptics Circle (#75) has four articles on alternative medicine.

Detox and Re-Tox: Bad Medicine and Even Worse Homeopathy at Alt-Med Mecca NewsTarget on The Bad Idea Blog.

Random reward may explain why homeopathy still exists on Med Journal Watch.

How we know what will kill or cure us on Junkfood Science.

Diluting the Profits on Skeptico.

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Irreducible Complexity

Lately I've run across several different definitions of irreducible complexity [Utterly Stupid Quote of the Day]. Most people seem to think that irreducible complexity is defined as something that cannot evolve but that's not the original definition [IDiot Logic].

Here's what Michael Behe says on page 39 of Darwin's Black Box.

By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.

Behe then goes on to say that an irreducibly complex system cannot evolve by natural selection.

The definition is not a problem. By this definition there are many irreducibly complex systems in biology. For example, the bacterial flagella is a pretty good example as long as you relax the criteria a little bit. (Some of the minor parts can easily be removed without affecting the overall function.)

The problem is not with the definition, it's with the conclusion. Irreducibly complex systems can easily evolve. All that's required is for the simpler intermediates to have some function other than the one seen in the final completed structure. In the case of the bacterial flagella this simpler function was secretion of large molecules. The flagella evolved from a type III secretion system by just adding a few extra components.

Thus, as Behe says above, it was not produced directly by continuously improving the initial function. Instead, there were several intermediate functions (e.g., secretion) that preceded the shift to the final function we observe today. This is how irreducibly complex systems evolve.

The citric acid cycle is another example of an irreducibly complex system for which there's an easily understood evolutionary pathway. The circular pathway arose when the ends of a forked pathway were joined by evolution of a single enzyme [Defining Irreducible Complexity].

Irreducible complexity is a concept invented by Intelligent Design Creationists. You'd think they would at least make the effort to understand something they created!

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My Moral Foundations

 
I took the Moral Foundations Questionnaire to see the basis of my morality. My score is shown in green and typical scores for liberals are colored blue. Conservatives are red. (Strange choice of colors, if you ask me.)


What does this mean? Not much really, although the people who run the test think it's important. Here's what they say ...

The scale is a measure of your reliance on and endorsement of five psychological foundations of morality that seem to be found across cultures. Each of the two parts of the scale contained four questions related to each foundation: 1) harm/care, 2) fairness/reciprocity (including issues of rights), 3) ingroup/loyalty, 4) authority/respect, and 5) purity/sanctity.

The idea behind the scale is that human morality is the result of biological and cultural evolutionary processes that made human beings very sensitive to many different (and often competing) issues. Some of these issues are about treating other individuals well (the first two foundations - harm and fairness). Other issues are about how to be a good member of a group or supporter of social order and tradition (the last three foundations). Haidt and Graham have found that political liberals generally place a higher value on the first two foundations; they are very concerned about issues of harm and fairness (including issues of inequality and exploitation). Political conservatives care about harm and fairness too, but they generally score slightly lower on those scale items. The big difference between liberals and conservatives seems to be that conservatives score slightly higher on the ingroup/loyalty foundation, and much higher on the authority/respect and purity/sanctity foundations.

This difference seems to explain many of the most contentious issues in the culture war. For example, liberals support legalizing gay marriage (to be fair and compassionate), whereas many conservatives are reluctant to change the nature of marriage and the family, basic building blocks of society. Conservatives are more likely to favor practices that increase order and respect (e.g., spanking, mandatory pledge of allegiance), whereas liberals often oppose these practices as being violent or coercive.

I love it when they talk about basic foundations of morality and the biological basis of morality and then give tests where people are all over the map. How can we have such differences between liberals and conservatives if these "foundations" are universal and innate? Does this mean that right-wing conservatives were born stupid and there's nothing they can do about it?

That's a scary thought.

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[Hat Tip: Gene Expression]

Canadian Students Are #3 in Science

 
The Organization for Economic Co-operation and Development (OECD) has a Programme for International Student Assessmant (PISA).

The first study was carried out in 2000 and it tested for reading ability. Canada ranked fourth in that survey, behind Korea, Finland, and Hong Kong–China.

The second study in 2003 measured mathematical ability and Canada was fifth. Only Chinese Taipei, Finland, Korea, and Hong Kong–China did better.

The 2006 study evaluated scientific literacy. Over 22,000 15-year-old Canadian students from more than 1,000 schools took part in the test. Canadian students ranked in third place behind Finland and Hong Kong-China. The chart (above, left) shows all countries that ranked significantly above the OECD average. The chart below lists some of the countries that were below average. In total, more than 400,000 students from 57 countries took the test.

The PISA study defined scientific literacy as ...

... an individual’s capacity to use scientific knowledge, to identify questions, and to draw evidence-based conclusions in order to understand and help make decisions about the natural world and the changes made to it through human activity.

Science competency was evaluated through a series of questions designed to elicit information on ...

1. Identifying scientific issues required students to recognize issues that can be explored scientifically and the key features of scientific investigation.

2. Explaining phenomena scientifically involved the application of the knowledge of science to describe or interpret phenomena scientifically and predict changes.

3. Using scientific evidence meant interpreting the evidence to draw conclusions; to explain them; to identify the assumptions, evidence, and reasoning that underpin them; and to reflect on their implications.

Students were assessed on two different kinds of scientific literacy ...

Knowledge of science. This entailed an understanding of fundamental scientific concepts and theories, in core scientific areas. The four content areas covered were “Physical systems,” “Living systems,” “Earth and space systems,” and “Technological systems,” representing key aspects of understanding the natural world.

Knowledge about science. This included understanding the purposes and nature of scientific enquiry and understanding scientific explanations, which are the results of scientific enquiry.

The complete Canadian Report can be found on the Council of Ministers of Education website. There's much more information about other countries on the PISA website.

In general, the study looks very good. The questions are excellent and the analysis seems scholarly and well-reasoned. There are no great surprises. Student performance is correlated with school funding levels and socio-economic level.

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The Golden Compass

 
This is a clip from The Golden Compass. It's the movie the Christians are afraid of. They want you to boycott it because it promotes atheism. It looks pretty good to me. I think I'd go see it even if it wasn't just to oppose the boycott.

BTW, I also liked The Chronicles of Narnia even though it had a Christian theme. I don't have much trouble separating fantasy from reality.

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Tangled Bank #94

 
The latest version of the Tangled Bank has been posted by Felicia Gilljam on Life before death [Tangled Bank #94].

Welcome to Tangled Bank #94! My name is Felicia and this is my blog, Life before death, in which I write about secularism, science and bees, with the occasional digression into other things. You may notice that there has been a bit of a gap in posting lately, but I’m back in the game now. Should anyone want to know more about myself (unlikely as that may seem), there’s an About link in the sidebar. But now, without further ado, let’s get on with the carnival!

For those who have difficulty submitting articles to Tangled Bank, let me remind you that you can mail URL's to host followed by the "at" symbol then tangledbank.net.

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Sandwalk Readers Are Left of Center

 
The results of last month's poll show that 70% of Sandwalk readers tend to be liberals or left wingers. I suppose that's not a big surprise. Most of us tend to read blogs that reflect our point of view on the world. This blog is not likely to appeal to those from the right wing of the political spectrum.

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Nobel Laureate: Hugo Theorell

 

The Nobel Prize in Physiology or Medicine 1955.

"for his discoveries concerning the nature and mode of action of oxidation enzymes"

Axel Hugo Theodor Theorell (1903 - 1982) received the Nobel Prize in Physiology or Medicine for his work on biological oxidation-reduction reactions. These reactions are catalyzed by oxidoreductases and they often involve the oxidation and reduction of various cofactors. One of these cofactors, FMN, was Monday's Molecule #54. Near the beginning of his scientific career, Theorell worked with "yellow enzyme." The yellow color was due to the presence of riboflavin which turned out to be the cofactor FMN. It was possible to follow the oxidation and reduction of the cofactor by observing the change in color from yellow to white as it was reduced.

Later on he worked with alcohol deydrogenase, an enzyme that couples the oxidation of organic molecules to the reduction of NAD⁺. At the time this cofactor was known as DPN⁺. Theorell developed fluorescence spectroscopic methods to measure these very fast reactions.

Theorell also worked with cytochrome c, a heme-containing electron carrier involved in oxidation-reduction reactions that transfer electrons from complex III to complex IV during membrane-associated electron transport in mitochondria. Theorell was aware of the α-helix discovered by Pauling & Corey and his first X-ray images of cytochrome c confirmed that the heme group was completely surrounded by α-helices.

The Nobel Prize is awarded by the Karolinska Institute and Theorell was the first scientist from that institute to receive a Nobel Prize.

THEME:

Nobel Laureates
The presentation speech was given by Professor E. Hammarsten of the Royal Caroline Institute.

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen.

The Collegium of Karolinska Institutet has this year awarded the Prize in Physiology or Medicine to Professor Hugo Theorell for his discoveries concerning the nature and mode of action of oxidative enzymes.

More than a hundred years ago the vast field of research within which Theorell's work has been carried out was opened up by a Swedish investigator, Berzelius, who advanced the concept of catalysis and postulated that vital reactions were brought about by means of catalysts, subsequently called enzymes.

Let us as an example consider sugar, dissolved in water. It is not acted upon by oxygen outside the organism, but in living cells it is rapidly broken down by means of oxygen and enzymes, with the simultaneous liberation of energy in a form suitable for use in further reactions.

During the latter part of the 19th century the catalysts postulated by Berzelius were detected - enzymes that quicken dull and sluggish molecules such as oxygen and sugar which will not spontaneously interact. The enzymes bring about this change in the behaviour of the sluggish molecules, called activation, by contacting them for a moment and then releasing them - now in an active form - into the whirls of the molecular dance where they originate new compounds. The enzyme will contact one molecule after another without itself being changed or directly participating in the dance. It is like a tool in a production line, activating the inert material delivered to it by the belt so that a maelstrom of rapid reaction is created beyond it. But such a maelstrom can never come to rest since other tools are soon encountered, each of which maintains the motion and adapts it to a new rhythm. Thus the substances to be metabolized are brought into a sequence of rapid transformations by a versatile machinery built up of strictly specific units, the enzymes.

It is of fundamental importance to know the nature and mode of action of everyone of these truly life-giving enzymes. Their number is still unknown but it is certainly very great - Berzelius' intuitive idea has been fully confirmed in this respect.

In this field a Swedish investigator has once again substantially enlarged our knowledge.

Hugo Theorell realized from the first the importance in scientific investigation of seizing and keeping the initiative. He has realized, too, that «live and let live» is a fertilizing principle for teamwork. The able must not for long remain mere collaborators. They must themselves show initiative and become independent activators. An enzyme can give life to sluggish material in such a way that a new independent enzyme is created. Theorell's scientific work deals with active enzymes, but he is himself an efficient activator on the more complex human level.

His first discovery was made during the period 1933-1935 which, as a Fellow of the Rockefeller Foundation, he spent with the foremost pioneer in enzyme research, Otto Warburg. He arrived with his own idea and with his own technical means of substantiating it. He now made his great classical discovery of the splitting and recombination of the yellow enzyme. «Meister der Enzymforschung», Warburg called him after this scientific achievement. Since then Theorell has illuminated and clarified our understanding of several of the enzymes necessary for life, and in a passionate search for truth and fact in science has spared neither thoroughness nor effort.

Following a logical plan of investigation and with continuous refinement of technique he has clarified and enlarged that field of knowledge in which he is an outstanding leader.

The iron atoms built into many oxidative enzymes constitute functional centres, and many aspects of their intricate linkages to other parts of the enzyme have been revealed, as well as other important routes for the transport of electrons involved in the functioning of oxidative enzymes. He and his collaborators have shed light on the iron-containing enzymes called peroxidases. Before Theorell began his investigations, our knowledge of these substances was little more than guesswork. The extremely high velocity of their reactions demanded the skilful application of a range of advanced technique. It can safely be predicted that the profound analyses thereby performed will be decisive for the future integration of the role of the peroxidase system into the pattern of action of living organisms. The function of another group of iron-containing enzymes, the cytochromes, began to emerge towards the end of the last century, and here again Theorell has achieved an incisive analysis. The nature and function of the muscle pigment were also established through his investigations. He showed it to be an oxygen reservoir which comes into action when the oxygen content of the blood is depleted. It is a source of a «second wind».

A most important part of Theorell's researches has been concerned with the velocities of enzyme reactions and the factors which influence them, factors which determine the directions into which the enzymes force the processes in living organisms. These experiments are not only of basic importance but may be considered model investigations in enzymology.

Professor Hugo Theorell. A fertile imagination. An undeviating and critical accuracy. An astonishing technical skill.

All scientists possess some of these attributes. Very few have all. You are one of these few. In accordance with your gifts you have chosen the most important of all tasks in biology. The purification and the characterization of enzymes are essential prerequisites for progress within the realm of biological research. You have managed to bring about a decisive advance in this fundamental field, and in so doing you have brilliantly taken up and tended the heritage from Berzelius.

On behalf of Karolinska Institutet I ask you to receive your Nobel Prize for Physiology or Medicine for 1955 from the hands of His Majesty the King.

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[Photo Credit: Karolinska Institute]

Does Blogging Hurt Your Chances of Getting Tenure?

 
Here are two examples of academics who blog and who didn't get tenure [Too Much Information?]. Neither of them are certain that their blogs had any effect on the tenure committee but who knows for sure?

There are many blogging Assistant Professors who got tenure so it can't be all that bad. My own feeling is that blogging takes up a lot of time and those who are up for tenure might be able to make better use of that time.

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[Hat Tip: Joshua Rosenau at Thoughts from Kansas (Science educator "Expelled!," Disco Inst remains silent)]

Sherri Shepard Is Doing It Again

 
Remember Sherri Shepherd of The View? She's the one who never thought about whether the Earth was flat [Sherri Shepherd of The View Doesn't Believe in Evolution].

Well, she's at it again. This time she claims that Christians pre-date the Romans and the Greeks. (You better watch this while you can because it will surely be removed as soon as ABC finds out about it.)

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[Hat Tip: Mike's Weekly Skeptic Rant]

A Simplistic Explanation of Evo-Devo

 
This is a one minute explanation of evo-devo by Chris Mims, Editor of Scientific American. According to Mims, evo-devo is the idea that there are regulatory genes making proteins that control the expression of other genes. Many species have homologous regulatory proteins.

Whaaaaa? If that's all there is to evo-devo then what the hell is all the fuss about?

PZ Myers seems to think it's pretty cool [Evo-devo in 60 seconds]. Apparently PZ even helped with the script [What Is Evo-Devo?]. Maybe PZ can explain why evo-devo is so important if this is all there is.

Click To Play

Maybe you can't read it in 60 seconds but I think the description of evolutionary-developmental biology on the Wikipedia site is far better than this video.

Of course no definition will excuse some of the nonsense that's being spouted in the name of evo-devo [Evo-Devo: Innovation and Robustness in Evolution].

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The Lehigh University Disclaimer

 
Someone drew my attention to the note posted on the website of the Dept. of Biological Sciences at Lehigh University [Department Position on Evolution and "Intelligent Design']. This is the department where Michael Behe is a tenured Profesor. Here's the complete statement.

Department Position on Evolution and "Intelligent Design"

The faculty in the Department of Biological Sciences is committed to the highest standards of scientific integrity and academic function. This commitment carries with it unwavering support for academic freedom and the free exchange of ideas. It also demands the utmost respect for the scientific method, integrity in the conduct of research, and recognition that the validity of any scientific model comes only as a result of rational hypothesis testing, sound experimentation, and findings that can be replicated by others.

The department faculty, then, are unequivocal in their support of evolutionary theory, which has its roots in the seminal work of Charles Darwin and has been supported by findings accumulated over 140 years. The sole dissenter from this position, Prof. Michael Behe, is a well-known proponent of "intelligent design." While we respect Prof. Behe's right to express his views, they are his alone and are in no way endorsed by the department. It is our collective position that intelligent design has no basis in science, has not been tested experimentally, and should not be regarded as scientific.

This is an excellent summary of the proper way to treat Intelligent Design Creationism. There's no doubt the statement was carefully crafted and it shows. Intelligent Design Creationism isn't science. That's why it won't be taught in university except as an example of pseudoscience. We need to get the word out about this. Some people (e.g., Denyse O'Leary, Bill Dembski) still haven't got the message. We don't reject Intelligent Design Creationism because it's religious, we reject it because it ain't science.

The statement is highly relevant to the discussions we're been having about Intelligent Design Creationists. Imagine that you were trying to get a Ph.D. in this department while advocating that your thesis work refuted evolution and supported intelligent design. Since intelligent design isn't science your chances of graduating aren't great.

Imagine that you were up for tenure in this department while maintaining that intelligent design was a viable scientific option. Good luck.

On the other hand, if you already have tenure then you have jumped these hurdles and your right to say silly things is protected by academic freedom. That right must be upheld at all costs.

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Pat Condell Takes on the Atheist Accommodationists

 
Here's some of what Pat Condell says at 4:20 into the video ...

Maybe you think the way to deal with this is to engage it in polite debate, to make all your little points and counter-points and show us all what a clever dick you are. And that'll be great fun for you.

And the good news is you don't even have to worry about someone like me damaging your cause because you haven't got a a cause. What you've got is a hobby.

If God exists, and I had any reason to ask him for anything, I think I'd probably ask him to save me from the curse of polite and deferential atheists.

And that's not even the best quotation. You should hear what comes after that!

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[Hat Tip: Dr. Joan Bushwell's Chimpanzee Refuge]

Should an Intelligent Design Creationist Be Denied Tenure?

 
The quick answer is, yes.

Guillermo Gonzalez was recently denied tenure in Iowa State's Dept. of Astronomy. It seems clear that part of the decision was based on Gonzalez's promotion of demonstably bad science; namely, Intelligent Design Creationism.

Mike Dunford spells it out on The Questionable Authority [The Discovery Institute and the Gonzalez Tenure Issue: Why Should Intelligent Design be Privileged?].

It is clear from the fragments of email that the Discovery Institute released that Gonzalez's colleagues believed - correctly - that Intelligent Design is not science, and that if Gonzalez believes otherwise it casts doubts on his understanding of science. They were not arguing that his belief in ID should be used against him just because he believes In ID. They were arguing that Gonzalez's belief in Intelligent Design is evidence that he has an incorrect understanding of science.

If a tenure candidate at an astronomy department were to argue that the moon is made of green cheese, it would not be unreasonable for the tenure committee to question the candidate's scientific credentials - and that candidate would be making a scientific argument that could be examined experimentally. Gonzalez doesn't even have that much going for him.

This is an important point. As Mike points out, the Discovery Institute is fond of promoting its work as "science" and it's proud to claim Guillermo Gonzalez as a bona fide scientist.

The Discovery Institute can't have it both ways. If it's science, then Gonzalez should be judged on the quality of his science, in which case he will be found wanting and denied tenure. If it's religion, then Gonzalez should not be making claims that his work is scientific and he should not put his creationist work on his CV.

In an effort to win an appeal, Gonzalez and his backers obtained email messages fro Professors in the Astronomy Department via the freedom of information act. Here's one email comment by Eli Rosenberg, the Chair of the Astronomy Department [see More on Gonzalez tenure denial].

... on numerous occasions, Dr. Gonzalez has stated that Intelligent Design is a scientific theory and someday would be taught in science classrooms. This is confirmed by his numerous postings on the Discovery Institute Web site. The problem here is that Intelligent Design is not a scientific theory. Its premise is beyond the realm of science. … But it is incumbent on a science educator to clearly understand and be able to articulate what science is and what it is not. The fact that Dr. Gonzalez does not understand what constitutes both science and a scientific theory disqualifies him from serving as a scienceeducator.

I see nothing wrong here. I looks to me like this is grounds for tenure denial.

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Gene Genie #21

 

The 21st edition of Gene Genie has just been published on Bayblab [Welcome to Gene Genie].

The next edition (#22) will appear here on Sandwalk on December 16th. Submit your entries at Blog Carnival by clicking on the link to Submit an Article. All you have to do is fill out a short form with the URL to your posting.

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