Is Acupuncture Better than Toothpicks?

 
Orac is at it again. He describes a pretty good study of the possible effects of acupuncture on lower back pain [Another acupuncture study misinterpreted]. The study showed that patients who got a sham procedure using toothpicks instead of needles reported the same "cure" as those who got two different versions of acupuncture.

In other words, acupuncture doesn't work. The scientific evidence is conclusive. Acupuncture is associated with a potent placebo effect but that's all. Patients can't tell the difference between needles and toothpicks. As long as they think they're getting the full-blown acupuncture treatment they'll report an improvement in lower back pain.

Here's the description of the toothpick technique that "cures" back pain.

Simulated acupuncture. We developed a simulated acupuncture technique using a toothpick in a needle guide tube, which was found to be a credible acupuncture treatment by acupuncture-naïve patients with back pain.Simulating insertion involved holding the skin taut around each acupuncture point and placing a standard acupuncture needle guide tube containing a toothpick against the skin. The acupuncturist tapped the toothpick gently, twisting it slightly to simulate an acupuncture needle grabbing the skin, and then quickly withdrew the toothpick and guide tube while keeping his or her fingers against the skin for a few additional seconds to imitate the process of inserting the needle to the proper depth. All acupuncture points were stimulated with toothpicks at 10 minutes (ie, the acupuncturist touched each acupuncture point with the tip of a toothpick without the guide tube and rotated the toothpick clockwise and then counterclockwise less than 30°) and again at 20 minutes just before they were "removed." To simulate withdrawal of the needle, the acupuncturist tightly stretched the skin around each acupuncture point, pressed a cotton ball firmly on the stretched skin, then momentarily touched the skin with a toothpick (without the guide tube) and quickly pulled the toothpick away using the same hand movements as in regular needle withdrawal. The acupuncturists simulated insertion and removal of needles at the 8 acupuncture points used in the standardized treatment.

Just about anyone could be trained to do this. Think of how much unnecessary back pain could be eliminated if spouses and friends would just poke each other with toothpicks!

I think I'll ask Ms. Sandwalk to try it next time my back hurts.

---

Monday's Molecule #121: Winner

 
UPDATE:The image is a 2D Nuclear magnetic resonance spectrum of cane sugar from the Nobel website. This kid of image can only be produced by mathematically transforming the primary data to create a multidimensional representation. Richard Ernst discovered the Fourier transform method that led to solving three dimensional structures by NMR. He won a Nobel Prize in 1991.

This week's winner is Michael Clarkson of Waltham MA (USA). The dominance of Canadians is coming to an end.

---

This is a true representation of the structure of a biological molecule but I don't expect you you to guess the molecule. Instead, you have to explain what this image is depicting and how it relates to a Nobel Laureate.

There is one Nobel Laureate who is most closely identified with this particular type of image. You have to identify the Nobel Laureate and what the prize was for. Be careful, because I'm looking for the pioneer in this field and not for other Nobel Prize winners who may have come later. Be sure to check the list of previous Nobel Laureates on Sandwalk.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison and Adam Santoro of the University of Toronto.

The Canadians are still ahead in the competition between Canadians the rest of the world but Dima and Laura are at least keeping it from being a total rout.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours. Comments are now open.

---

Monday's Molecule #121

 
This is a true representation of the structure of a biological molecule but I don't expect you you to guess the molecule. Instead, you have to explain what this image is depicting and how it relates to a Nobel Laureate.

There is one Nobel Laureate who is most closely identified with this particular type of image. You have to identify the Nobel Laureate and what the prize was for. Be careful, because I'm looking for the pioneer in this field and not for other Nobel Prize winners who may have come later. Be sure to check the list of previous Nobel Laureates on Sandwalk.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison and Adam Santoro of the University of Toronto.

The Canadians are still ahead in the competition between Canadians the rest of the world but Dima and Laura are at least keeping it from being a total rout.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

---

E.O. Wilson in New York

It was Saturday morning and I was in the offices of the New York Academy of Sciences on the 40th floor of 7 World Trade Center. The view to the East was spectacular. We could see the Brooklyn bridge and the 59th Street bridge with Brooklyn and Queen's in the background.

I love cities, I love the tall buildings and the hustle and bustle of the street life.

E.O. Wilson was about to kick off the opening session of The Two Cultures in the 21st Century. I had never heard him in person so I grabbed a good seat and settled down.

Most of his talk was about imaging the brain, behaviorial psychology, and evolutionary psychology. His main point was that scientists are learning a lot about how the brain works and this brings together the humanities and science. E.O. Wilson favors consilience.

Let me give you one example from his talk to illustrate the concept. Wilson talked about a study that was done to determine the ideal environment for humans. People were asked to identify their favorite scenes and the results were used to derive a composite view of what the ideal human environment would look like.

Wilson illustrated it with a slide taken from the third or fourth floor of the John Deere headquarters in Illinois. The view showed extensive grasslands with some water in the foreground. The trees had large branches that were almost parallel to the ground. Massive abstract sculptures evoked an image of large animals.

According to Wilson, this idealized environment is an ancient memory of the environment where we evolved. Our ancestors lived in caves on a cliff side overlooking a savanna full of large animals. The trees of the savanna have branches that are almost parallel to the ground. We like to have water nearby. This is why the typical modern human prefers that type of environment. Science and beauty come together.

Here's how Wilson describes it in The Creation: An Appeal to Save Life on Earth pp. 66-67.

…Researchers have found that when people of different cultures, including those of North America, Europe, Asia and Africa, are given freedom to select the setting of their homes and work places, they prefer an environment that combines three features. They wish to live on a height looking down and out, to scan a parkland with scattered trees and copses spread before them, closer in appearance to a savanna than either a grassland or a closed forest, and to be near a body of water, such as a lake, river, or sea. Even if all these elements are purely aesthetic and not functional, as in vacation homes, people who have the means will pay a very high price to obtain them.

There is more. Subjects in choice tests prefer their habitation to be a retreat, with a wall, cliff, or something else solid to the rear. They want a view of fruitful terrain in front of the retreat. They like large animals scattered thereabout, either wild or domestic. Finally, they favour trees with low horizontal branches and divided leaves. It is probably not a coincidence that some people, I among them, consider the Japanese Maple the world’s most beautiful tree.

These quirks of human nature do not prove but are at least consistent with the savanna hypothesis of human evolution. Supported by considerable evidence from fossil record, this interpretation holds that human beings today still choose the habitats resembling those in which our species evolved in Africa during millions of years of prehistory.

I realized then and there that I was a strange sort of human. My love of cities must be some kind of aberration. I also realized in an instant that all of my mother's ancestors from the past 2000 years must have been desperately unhappy. They all come from Northern Europe where they lived in clusters of small farms in rolling hills covered in dense forest. The only thing they had going for them was the presence of large animals in the barns. How sad.

---

[Photo Credit: ©John Deere (John Deere Attractions)]

New York City: Theater and Dinner

 

---

The Human Genome Sequence Is not Complete

 
The latest version of the human genome sequence is called Build 36 or GRCh37. Here's an overview from the Genome Reference Consortium.


The large red triangles represent regions where there is a lot of variability so that no single representation of the genome sequence will describe a majority of humans.

The black regions represent parts of the chromosomes that have not been sequenced and assembled into long stretches (contigs) of reliable sequence. Most of the unsequenced regions are at centromeres, or telomeres, or on the Y chromosome. These regions consist of thousands of copies of highly repetitive DNA. It is impossible to assemble these repetitive sequences.

Scientists are urging that more attention be focused on completing the chimpanzee and macaque genome sequences. We have been waiting a long time for the draft sequences of those genomes to be finished. The explosion of data on the human genome can only be realistically evaluated by comparing it to our closest relatives. (For example, are human non-coding RNAs conserved in primates?)

The fact that the human genome is not complete is not a problem. We know what's in the repetitive sequence regions even though we don't know exactly how it is arranged. The effort required to finish of the last bit is probably not as important as getting a final draft of other sequences.

Sandra Porter wonders Why don't we finish the human genome first?.

---

Jason Rosenhouse Doesn't Understand Pluralists

 
Jason Rosenhouse has posted some comments on a recent book review by Richard Lewontin. In that book review, Lewontin—who along with Gould is the co-author of the spandrels paper—questions the emphasis on natural selection and the use pf "Darwinism" as a synonym for evolution. Read Lewontin on Darwin to see what Jason thinks of the book review.

I want to focus on a specific question that Jason Rosenhouse asks.

I've never really understood what it is exactly that anti-selectionists are complaining about. If they agree that complex adapations arise as the result of gradual accretion mediated by natural selection, then I fail to see how they are really so different from people like Richard Dawkins or Daniel Dennett (two people often described as being beknighted uber-selectionists). If they do not agree then I would like to hear their proposed alternative mechanism.

The original paper by Gould and Lewontin, The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme, explains the problem very well. The authors begin their criticism with ...

We wish to question a deeply engrained habit of thinking among students of evolution. We call it the adaptationist programme, or the Panglossian paradigm. It is rooted in a notion popularized by A.R. Wallace and A. Weismann, (but not, as we shall see, by Darwin) toward the end of the nineteenth century: the near omnipotence of natural selection in forging organic design and fashioning the best among possible worlds. This programme regards natural selection as so powerful and the constraints upon it so few that direct production of adaptation through its operation becomes the primary cause of nearly all organic form, function, and behavior. Constraints upon the pervasive power of natural selection are recognized of course (phyletic inertia primarily among them, although immediate architectural constraints, as discussed in the last section, are rarely acknowledged). But they are usually dismissed as unimportant or else, and more frustratingly, simply acknowledged and then not taken to heart and invoked.

The anti-selectionists—I am one—do not question the fact that adaptations are produced by natural selection. What we question is whether everything in evolution is an adaptation. We question those who think that "evolution" and "natural selection" are synonyms. And since "Darwinism" is equivalent to evolution by natural selection we question whether evolution is the same as Darwinism.

We pluralists like to point out that much of evolution is due to random genetic drift. Since Darwin's name is not associated with the theory of evolution by random genetic drift, it is inappropriate to say that all of evolution is Darwinist.

It's not that complicated. It was all explained in the classic spandrels paper published 30 years ago. Complex biological structures may be due entirely to adaptation, or they may be mostly an accident that's arisen by random genetic drift, or they may be due to combinations of drift and selection.

---

What do protein crystallographers dream of?

 
"What do protein crystallographers dream of?" is the question asked by Ananyo Bhattacharya in an article published in Nature [Protein structures: Structures of desire].

The structures of many protein complexes have been determined but crystallographers have a list of holy grails that, so far, have eluded them. It's an interesting list and one that I mostly agree with. Can you identify the structure shown here in cartoon form?

One glaring omission is pyruvate dehydrogenase. Lot's of people want to see that structure. Other notable omissions include complex I of the membrane-associated electron transport chain and the protein import complex of the endoplasmic reticulum. Don't protein crystallographers dream of those?

---

The Biology Textbooks Are Wrong?

 
The other day I suggested that Casey Luskin was probably just ignorant. Unlike other creationists, he problably isn't a liar. Today I'm not so sure.



What is it with FOX news?

---

Win Free Prizes from Denyse O'Leary

 
Every week there are dozens of people who try to guess Monday's Molecule and win a free lunch with me. Now, that's a valuable prize—it's no wonder that so many people are trying to win.

Now you've got another chance to win valuable prizes. Denyse O'Leary is giving out prizes for people who comment on Uncommon Descent [Earn free stuff!: The Uncommon Descent Contest].

What are the prizes?

• 10 DVDs of Expelled,courtesy the producers.
• 10 DVDs of Privileged Planet, courtesy the producers.
• 5 subscriptions, including back issues, to the excellent Christian/theistic science and culture mag, Salvo, complete with recent back issues, courtesy the editor-in-chief.

Looks like I've got serious competition!

Here's the first contest question: Does the multiverse help science make sense - or simply destroy science?. Hmmm ... I wonder what the right answer is?

---

Casey Luskin Writes About the Universal Common Ancestor

 
Casey Luskin is writing about the tree of life and the universal common ancestor. The second installment in a series of five posting is here.

When speaking to the public, evolutionists are infamous for overstating the evidence for universal common ancestry. For example, when speaking before the Texas State Board of Education in January, 2009, University of Texas evolutionist biologist David Hillis cited himself as one of the “world’s leading experts on the tree of life” and later told the Board that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. But this is not accurate. Indeed, in the technical scientific literature, one finds a vast swath of scientific papers that have found contradictions, inconsistencies, and flat out failures of the molecular data to provide a clear picture of phylogenetic history and common descent.

Indeed, the cover story of the journal New Scientist, published on the very day that Dr. Hillis testified, was titled, “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’ gross oversimplification of molecular systematics, the article reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart:

It's true that things are very confusing at the base of the tree of life. The evidence indicates that genes were frequently exchanged between primitive prokaryotic species and this means there is no single tree that represents all of life.

But this doesn't negate the idea of a universal common ancestor. The origin of life could still be a unique event that gave rise over millions of years to many different descendants that subsequently exchanged genes. Or, there may have been a few independent origins of life.

The available evidence shows that most fundamental properties of life are shared by all living things (e.g. basic metabolic pathways, genetic code). This is consistent with a unique origin of life but it's also consistent with multiple origins as long as only one version of each process has survived. The odds favor a single origin and a universal common ancestor.

What's interesting about Luskin's article is that he is hopelessly confused about the difference between a phylogenetic tree and the origin or life. He seems to think that a bushy tree with many interconnecting branches rules out a universal common ancestor. I don't know what he postulates in its place unless the idea of God creating three or four different primitive prokaryotes is what appeals to him more than God just doing it once.

Intelligent Design Creationists come in many different flavors. Often it's hard to decide whether they are being deceptive (lying) or just ignorant. I think that Casey Luskin is just ignorant. He finds it difficult to make a coherent argument and he doesn't take the time to learn more about his subject. In that sense, he's much less dangerous than Jonathan Wells.

---

Call a Canadian!!

 
Dear Americans,

Have you ever thought about asking an average Canadian what they think of their health care system? Read Call a Canadian on Effect Measure.

---

Oops! Did New Scientist Goof Again?

 
New Scientist published an article on Science and art: Still two cultures divided?.

The journal invited six people to comment on the two cultures. Here's the list ....

• Stefan Collini is a professor of literature and intellectual history at the University of Cambridge. He edited The Two Cultures (1993, CUP)
• Susan Haack is a professor of philosophy and a professor of law at the University of Miami, Florida
• Harry Collins is professor of sociology at Cardiff University in the UK
• Mary Midgley is a philosopher and writer
• Sandra Harding is a philosopher and professor of education at the University of California, Los Angeles
• A. C. Grayling is a professor of philosophy at Birkbeck, University of London

A perceptive commenter (Khoo) asks, "Why was an entire article written about the divide between the arts and the sciences, and not a single physical scientist or mathematician interviewed? Does the author believe these scientists have nothing to say about the arts?"

Good point. A classic demonstration of the two cultures in action.

---

Atheists Serve the Devil!

 

Who knew? I wonder what the Devil eats for lunch? If I'm going to serve him I'd better find out.

Is he a big tipper?

This is Pat Robertson responding to a question. A caller wants to know how she, a Christian, can get along with her boyfriend, an atheist. Can you guess how the good Christian responds? Think about it, then watch.

---

[Hat Tip: Friendly Atheist]

How to Frame a Null Hypothesis

A reader has alerted me to an article by Michael White at Adaptive Complexity: Genomic Junk and Transcriptional Noise.

With hot, new technologies, biologists are taking higher-resolution snapshots of what's going on inside the cell, but the results are stirring up controversy. One of the most interesting recent discoveries is that transcription is everywhere: DNA is transcribed into RNA all over the genome, even DNA that has long been thought to have a non-functional role. What is all of this transcription for? Does the 'dark matter' of the genome have some cryptic, undiscovered function?

Unfortunately, in all of the excitement over possible new functions, many biologists have forgotten how to frame a null hypothesis - the default scenario that you expect to see if there is no function to this transcribed DNA. As a result, the literature is teeming with wild, implausible speculation about how our excess DNA might be beneficial to us.

So here, let's step back and look at what we expect from DNA when it's playing absolutely no functional role; in other words, let's look at the null hypothesis of genomic junk and transcriptional noise. We can then take our null hypothesis and use it to look at a fascinating new study of how genomic parasites sculpt transcription in our cells.

If you are interested in what's wrong with science these days then you must read his article.

The point is not whether you believe that all transcription is adaptive and functional, or whether you believe that most of it is noise. The real point is that it is very bad science to ignore the null hypothesis and publish naive speculation as if it were the only possible explanation.

Whenever you see a paper that fails to address the null hypothesis you can be sure that you are reading bad science. Everything else in the paper is suspect.

The key fact that most scientists are overlooking is that RNA polymerase and the various transcription factors must bind non-specifically at thousands of sites in a random sequence of junk DNA. This is just basic biochemistry of the sort that should be taught in undergraduate classes. Transcription will be initiated by accident at some of these sites even though they are not functional promoters. Again, this is basic biochemistry.

---

[Image Credit: Horton et al. Principles of Biochemistry 4/e p.657]